Fri Mar 29 20:18:02 UTC 2024 I: starting to build pyranges/unstable/armhf on jenkins on '2024-03-29 20:17' Fri Mar 29 20:18:02 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_33/10871/console.log Fri Mar 29 20:18:03 UTC 2024 I: Downloading source for unstable/pyranges=0.0.111+ds-7 --2024-03-29 20:18:03-- http://deb.debian.org/debian/pool/main/p/pyranges/pyranges_0.0.111%2bds-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2428 (2.4K) [text/prs.lines.tag] Saving to: ‘pyranges_0.0.111+ds-7.dsc’ 0K .. 100% 6.85M=0s 2024-03-29 20:18:03 (6.85 MB/s) - ‘pyranges_0.0.111+ds-7.dsc’ saved [2428/2428] Fri Mar 29 20:18:03 UTC 2024 I: pyranges_0.0.111+ds-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pyranges Binary: python3-pyranges Architecture: all Version: 0.0.111+ds-7 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Étienne Mollier Homepage: https://github.com/biocore-ntnu/pyranges Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/pyranges Vcs-Git: https://salsa.debian.org/med-team/pyranges.git Testsuite: autopkgtest-pkg-python Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-ncls , python3-pyrle , python3-pytest , python3-pytest-xdist , python3-sorted-nearest, python3-hypothesis, bedtools, samtools Package-List: python3-pyranges deb python optional arch=all Checksums-Sha1: 3591cd303505955df6c34eec755d51f27bd38e5b 3288424 pyranges_0.0.111+ds.orig.tar.xz bbf602d834d8e2ce67c1029b2e561f00d39e8589 83796 pyranges_0.0.111+ds-7.debian.tar.xz Checksums-Sha256: b22a50cb9e0109c8c14720385a5e87bef029f491d4f3e02dbe492866802144d1 3288424 pyranges_0.0.111+ds.orig.tar.xz e03b1b53d8cc25d6e94ac62b0dc6eb455e56a8ab0c6018a106c43b07e36c429e 83796 pyranges_0.0.111+ds-7.debian.tar.xz Files: 2c48870491f89e171b4aeeaa5b3b216a 3288424 pyranges_0.0.111+ds.orig.tar.xz 31ddf7357517790430841c5fdcf32de1 83796 pyranges_0.0.111+ds-7.debian.tar.xz Dgit: 334ec47f92336819696f8e033c7c690a17174f2f debian archive/debian/0.0.111+ds-7 https://git.dgit.debian.org/pyranges -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmXYxM0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdol0Q//b9TWLQmeyLiC7Ugi1QqlvOflrQCx 46DBSrymgC8Q043RiOd5i/Kx6nmsoy58mifXRndO09oTWQAw4lMbGM3q/nMmDid2 2jHDcN5SwFsP7fWj2diIQDJ4vcMRU6twAFDPwKX+yJD08X4f2PTLYJsKptqvoRLP 4by1J0TR1rU5jjrqeQCzaR2jCGEIOSSk6CZJ9N+1T+7KvHQ1pqS345AVS6zzluza l/ppJVV+wviWPSabBGzfhZ4lTrXjWUqEewfgswJV5RGtOSa3cZxwgXUdn6KFyFYW 4Zd5BsnWJ/VWMSUlOoIfO6EN+ghH8MQ/kzzkWFhSyngdsL7VrTWt0fWlc1kvMKDS GwzexnKN/XNHYV1V9vozrWWubRmlMZMJXTad+po+lNbAPOLGd7T+bP93x2l/Ftm0 GkdPitN8Y9EJquxG2wF40wtzQfmoi8AfuI28s7mB1aFlfsVmC5Z/z/ZwDsZ5craU f4zLjdipsCsKLHAaSi6ded35M+pNIrMpCbwmzjY2kxdhVLWCPhnlhMzKrqxWknLN YKcUs0olHOyGIjwoq+5U8o6ZQuMYLwY9+3kizyobgJ/AYaxvOgXi9LgbaBmhG/2I pmn2LdFudnjKvmSckJzQSuIZowpeZwL5USqyD8JCDxQn1Cc3J+B0ZO2TBMBUpTkv rP3I2BS8O18Kx4M= =JH6d -----END PGP SIGNATURE----- Fri Mar 29 20:18:03 UTC 2024 I: Checking whether the package is not for us Fri Mar 29 20:18:03 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Fri Mar 29 20:18:03 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Sat Mar 30 14:18:33 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 29 08:18:19 -12 2024 I: pbuilder-time-stamp: 1711743499 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pyranges_0.0.111+ds-7.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-7.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Feb 23 16:16:13 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyranges_0.0.111+ds-7.dsc: no acceptable signature found dpkg-source: info: extracting pyranges in pyranges-0.0.111+ds dpkg-source: info: unpacking pyranges_0.0.111+ds.orig.tar.xz dpkg-source: info: unpacking pyranges_0.0.111+ds-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_dtype.patch dpkg-source: info: applying reorder.patch dpkg-source: info: applying numpy_1.24.patch dpkg-source: info: applying healthcheck-all.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying pandas2.0.patch dpkg-source: info: applying fix-test_unary.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9885/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='cd031ba573034df8b5c112e75fdee3ed' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='9885' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.agdnyIhO/pbuilderrc_tcJh --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.agdnyIhO/b1 --logfile b1/build.log pyranges_0.0.111+ds-7.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32z 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 28 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/9885/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-ncls, python3-pyrle, python3-pytest, python3-pytest-xdist, python3-sorted-nearest, python3-hypothesis, bedtools, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19467 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-ncls; however: Package python3-ncls is not installed. pbuilder-satisfydepends-dummy depends on python3-pyrle; however: Package python3-pyrle is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-sorted-nearest; however: Package python3-sorted-nearest is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-dateutil{a} python3-distutils{a} python3-execnet{a} python3-hypothesis{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-natsort{a} python3-ncls{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyrle{a} python3-pytest{a} python3-pytest-xdist{a} python3-setuptools{a} python3-six{a} python3-sorted-nearest{a} python3-sortedcontainers{a} python3-tabulate{a} python3-tz{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx publicsuffix python3-bottleneck python3-bs4 python3-click python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget 0 packages upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 51.6 MB of archives. After unpacking 214 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.11-minimal armhf 3.11.8-3+b3 [804 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf python3.11-minimal armhf 3.11.8-3+b3 [1600 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-4 [145 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf libpython3.11-stdlib armhf 3.11.8-3+b3 [1703 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf python3.11 armhf 3.11.8-3+b3 [597 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf libpython3.12-minimal armhf 3.12.2-4+b2 [794 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf python3.12-minimal armhf 3.12.2-4+b2 [1739 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-3+b1 [1091 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.39.3-11 [82.5 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.7-1+b2 [33.4 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.12.0-3+b2 [1367 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf bedtools armhf 2.31.1+dfsg-2 [578 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-1 [183 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b1 [106 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf python3-lib2to3 all 3.12.2-3 [77.6 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf python3-distutils all 3.12.2-3 [131 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf python3-pkg-resources all 68.1.2-2 [241 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf python3-setuptools all 68.1.2-2 [468 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf dh-python all 6.20240310 [106 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.0-2.4 [19.5 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.20.1-6+b1 [30.6 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.20.1-6+b1 [75.5 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 58 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.20.1-6+b1 [290 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.20.1-6+b1 [112 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.59.0-1+b1 [62.7 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b3 [53.2 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.0-4.1+b1 [198 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.7.1-1 [383 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14-20240315-1 [264 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libhts3t64 armhf 1.19+ds-1.1+b1 [395 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.4+20240113-1 [81.8 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libpython3.12-stdlib armhf 3.12.2-4+b2 [1790 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf python3.12 armhf 3.12.2-4+b2 [653 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf python3-all armhf 3.11.8-1 [1056 B] Get: 74 http://deb.debian.org/debian unstable/main armhf python3-attr all 23.2.0-2 [65.5 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf python3-six all 1.16.0-6 [16.3 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf python3-dateutil all 2.9.0-2 [79.4 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf python3-execnet all 2.0.2-1 [37.2 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf python3-hypothesis all 6.99.9-1 [312 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 81 http://deb.debian.org/debian unstable/main armhf python3-natsort all 8.0.2-2 [39.0 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf python3-numpy armhf 1:1.26.4+ds-6 [4131 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf python3-ncls armhf 0.0.63-hotfix+ds-1+b4 [437 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf python3-packaging all 23.2-1 [44.8 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf python3-tz all 2024.1-2 [30.9 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf python3-pandas-lib armhf 2.1.4+dfsg-5 [7000 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf python3-pluggy all 1.4.0-1 [26.2 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf python3-tabulate all 0.8.10-1 [38.8 kB] Get: 90 http://deb.debian.org/debian unstable/main armhf python3-pyrle armhf 0.0.33-4.1 [313 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf python3-pytest all 8.1.1-1 [245 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf python3-pytest-xdist all 3.5.0-1 [42.1 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf python3-sorted-nearest armhf 0.0.39+dfsg-2 [488 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf samtools armhf 1.19.2-1+b1 [614 kB] Fetched 51.6 MB in 1s (91.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19467 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-3+b3_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.8-3+b3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-3+b3_armhf.deb ... Unpacking python3.11-minimal (3.11.8-3+b3) ... Setting up libpython3.11-minimal:armhf (3.11.8-3+b3) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-3+b3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19785 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_armhf.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../5-libreadline8t64_8.2-4_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-3+b3_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.8-3+b3) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-3+b3_armhf.deb ... Unpacking python3.11 (3.11.8-3+b3) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20779 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_armhf.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:armhf. Preparing to unpack .../01-libpython3.12-minimal_3.12.2-4+b2_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.2-4+b2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../02-python3.12-minimal_3.12.2-4+b2_armhf.deb ... Unpacking python3.12-minimal (3.12.2-4+b2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-3+b1_armhf.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.39.3-11_armhf.deb ... Unpacking bsdextrautils (2.39.3-11) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../11-libpipeline1_1.5.7-1+b2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.0-3+b2_armhf.deb ... Unpacking man-db (2.12.0-3+b2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package bedtools. Preparing to unpack .../18-bedtools_2.31.1+dfsg-2_armhf.deb ... Unpacking bedtools (2.31.1+dfsg-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../19-libdebhelper-perl_13.15.3_all.deb ... 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Preparing to unpack .../25-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../26-libelf1t64_0.191-1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.15-1+b1_armhf.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../28-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../29-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../33-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../34-python3-lib2to3_3.12.2-3_all.deb ... Unpacking python3-lib2to3 (3.12.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../35-python3-distutils_3.12.2-3_all.deb ... Unpacking python3-distutils (3.12.2-3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../36-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../37-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../38-dh-python_6.20240310_all.deb ... Unpacking dh-python (6.20240310) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../39-libblas3_3.12.0-3_armhf.deb ... Unpacking libblas3:armhf (3.12.0-3) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../40-libbrotli1_1.1.0-2+b3_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../41-libcom-err2_1.47.0-2.4_armhf.deb ... Unpacking libcom-err2:armhf (1.47.0-2.4) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../42-libkrb5support0_1.20.1-6+b1_armhf.deb ... Unpacking libkrb5support0:armhf (1.20.1-6+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../43-libk5crypto3_1.20.1-6+b1_armhf.deb ... Unpacking libk5crypto3:armhf (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../44-libkeyutils1_1.6.3-3_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../45-libkrb5-3_1.20.1-6+b1_armhf.deb ... Unpacking libkrb5-3:armhf (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../46-libgssapi-krb5-2_1.20.1-6+b1_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../47-libnghttp2-14_1.59.0-1+b1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.59.0-1+b1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../48-libpsl5t64_0.21.2-1.1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../49-librtmp1_2.4+20151223.gitfa8646d.1-2+b3_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b3) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../50-libssh2-1t64_1.11.0-4.1+b1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.0-4.1+b1) ... Selecting previously unselected package libcurl3t64-gnutls:armhf. Preparing to unpack .../51-libcurl3t64-gnutls_8.7.1-1_armhf.deb ... Unpacking libcurl3t64-gnutls:armhf (8.7.1-1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../52-libdeflate0_1.20-1_armhf.deb ... Unpacking libdeflate0:armhf (1.20-1) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../53-libgfortran5_14-20240315-1_armhf.deb ... Unpacking libgfortran5:armhf (14-20240315-1) ... Selecting previously unselected package libhtscodecs2:armhf. 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Selecting previously unselected package python3-all. Preparing to unpack .../60-python3-all_3.11.8-1_armhf.deb ... Unpacking python3-all (3.11.8-1) ... Selecting previously unselected package python3-attr. Preparing to unpack .../61-python3-attr_23.2.0-2_all.deb ... Unpacking python3-attr (23.2.0-2) ... Selecting previously unselected package python3-six. Preparing to unpack .../62-python3-six_1.16.0-6_all.deb ... Unpacking python3-six (1.16.0-6) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../63-python3-dateutil_2.9.0-2_all.deb ... Unpacking python3-dateutil (2.9.0-2) ... Selecting previously unselected package python3-execnet. Preparing to unpack .../64-python3-execnet_2.0.2-1_all.deb ... Unpacking python3-execnet (2.0.2-1) ... Selecting previously unselected package python3-sortedcontainers. Preparing to unpack .../65-python3-sortedcontainers_2.4.0-2_all.deb ... Unpacking python3-sortedcontainers (2.4.0-2) ... Selecting previously unselected package python3-hypothesis. Preparing to unpack .../66-python3-hypothesis_6.99.9-1_all.deb ... Unpacking python3-hypothesis (6.99.9-1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../67-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-natsort. Preparing to unpack .../68-python3-natsort_8.0.2-2_all.deb ... Unpacking python3-natsort (8.0.2-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../69-python3-numpy_1%3a1.26.4+ds-6_armhf.deb ... Unpacking python3-numpy (1:1.26.4+ds-6) ... Selecting previously unselected package python3-ncls. Preparing to unpack .../70-python3-ncls_0.0.63-hotfix+ds-1+b4_armhf.deb ... Unpacking python3-ncls (0.0.63-hotfix+ds-1+b4) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../71-python3-packaging_23.2-1_all.deb ... Unpacking python3-packaging (23.2-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../72-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-pandas-lib:armhf. Preparing to unpack .../73-python3-pandas-lib_2.1.4+dfsg-5_armhf.deb ... Unpacking python3-pandas-lib:armhf (2.1.4+dfsg-5) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../74-python3-pandas_2.1.4+dfsg-5_all.deb ... Unpacking python3-pandas (2.1.4+dfsg-5) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../75-python3-pluggy_1.4.0-1_all.deb ... Unpacking python3-pluggy (1.4.0-1) ... Selecting previously unselected package python3-tabulate. Preparing to unpack .../76-python3-tabulate_0.8.10-1_all.deb ... Unpacking python3-tabulate (0.8.10-1) ... Selecting previously unselected package python3-pyrle. Preparing to unpack .../77-python3-pyrle_0.0.33-4.1_armhf.deb ... Unpacking python3-pyrle (0.0.33-4.1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../78-python3-pytest_8.1.1-1_all.deb ... Unpacking python3-pytest (8.1.1-1) ... Selecting previously unselected package python3-pytest-xdist. Preparing to unpack .../79-python3-pytest-xdist_3.5.0-1_all.deb ... Unpacking python3-pytest-xdist (3.5.0-1) ... Selecting previously unselected package python3-sorted-nearest. Preparing to unpack .../80-python3-sorted-nearest_0.0.39+dfsg-2_armhf.deb ... Unpacking python3-sorted-nearest (0.0.39+dfsg-2) ... Selecting previously unselected package samtools. Preparing to unpack .../81-samtools_1.19.2-1+b1_armhf.deb ... Unpacking samtools (1.19.2-1+b1) ... Setting up libhtscodecs2:armhf (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-1+b2) ... Setting up libkeyutils1:armhf (1.6.3-3) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-11) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libpython3.12-minimal:armhf (3.12.2-4+b2) ... Setting up libpsl5t64:armhf (0.21.2-1.1) ... Setting up libnghttp2-14:armhf (1.59.0-1+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:armhf (1.47.0-2.4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:armhf (0.191-1) ... Setting up libkrb5support0:armhf (1.20.1-6+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Mar 29 20:19:03 UTC 2024. Universal Time is now: Fri Mar 29 20:19:03 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b3) ... Setting up libncurses6:armhf (6.4+20240113-1) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:armhf (1.20.1-6+b1) ... Setting up libgfortran5:armhf (14-20240315-1) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:armhf (1.20.1-6+b1) ... Setting up libssh2-1t64:armhf (1.11.0-4.1+b1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.2-4+b2) ... Setting up liblapack3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Setting up libreadline8t64:armhf (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libpython3.12-stdlib:armhf (3.12.2-4+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.8-3+b3) ... Setting up python3.12 (3.12.2-4+b2) ... Setting up libcurl3t64-gnutls:armhf (8.7.1-1) ... Setting up man-db (2.12.0-3+b2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:armhf (1.19+ds-1.1+b1) ... Setting up libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3.11 (3.11.8-3+b3) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-natsort (8.0.2-2) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-six (1.16.0-6) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pluggy (1.4.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-execnet (2.0.2-1) ... Setting up python3-lib2to3 (3.12.2-3) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.2-3) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-pytest (8.1.1-1) ... Setting up python3-hypothesis (6.99.9-1) ... Setting up python3-tabulate (0.8.10-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-numpy (1:1.26.4+ds-6) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b4) ... Setting up dh-python (6.20240310) ... Setting up python3-pytest-xdist (3.5.0-1) ... Setting up python3-pandas-lib:armhf (2.1.4+dfsg-5) ... Setting up python3-sorted-nearest (0.0.39+dfsg-2) ... Setting up python3-pandas (2.1.4+dfsg-5) ... Setting up python3-pyrle (0.0.33-4.1) ... Processing triggers for libc-bin (2.37-15.1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-7_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:305: python3.12 setup.py clean 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:305: python3.11 setup.py clean 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:305: python3.12 setup.py config I: pybuild base:305: python3.11 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:305: /usr/bin/python3.12 setup.py build I: pybuild base:305: /usr/bin/python3 setup.py build debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyranges-0.0.111+ds' echo 'Generating corresponding files ...' Generating corresponding files ... cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai make[1]: Leaving directory '/build/reproducible-path/pyranges-0.0.111+ds' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/*.bed /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/test_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges '/build/reproducible-path/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/chip_10.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/gencode.gff3' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/exons.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/bw.bw' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/cpg.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/lamina.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam.bai' I: pybuild base:305: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 4 ============================= test session starts ============================== platform linux -- Python 3.12.2, pytest-8.1.1, pluggy-1.4.0 -- /usr/bin/python3.12 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/.hypothesis/examples')) rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: hypothesis-6.99.9, xdist-3.5.0 created: 4/4 workers 4 workers [531 items] scheduling tests via LoadScheduling tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_binary.py::test_nearest[downstream-False-same] tests/data/test_data.py::test_all_data [gw1] [ 0%] PASSED tests/data/test_data.py::test_all_data tests/test_binary.py::test_set_intersect[False] [gw3] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] [gw0] [ 0%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] [gw3] [ 0%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] [gw1] [ 0%] FAILED tests/test_binary.py::test_set_intersect[False] tests/test_binary.py::test_set_intersect[same] [gw2] [ 1%] FAILED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_nearest[downstream-False-opposite] [gw0] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] [gw3] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] [gw1] [ 1%] FAILED tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_set_union[False] [gw2] [ 1%] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_binary.py::test_jaccard[False] [gw0] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] [gw3] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] [gw1] [ 2%] FAILED tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_set_union[same] [gw2] [ 2%] FAILED tests/test_binary.py::test_jaccard[False] tests/test_binary.py::test_jaccard[same] [gw0] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] [gw3] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] [gw1] [ 3%] FAILED tests/test_binary.py::test_set_union[same] tests/test_binary.py::test_overlap[False] [gw2] [ 3%] FAILED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw0] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] [gw3] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] [gw0] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] [gw1] [ 4%] PASSED tests/test_binary.py::test_overlap[False] tests/test_binary.py::test_overlap[same] [gw2] [ 4%] PASSED tests/test_binary.py::test_join[False] tests/test_binary.py::test_join[same] [gw3] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] [gw0] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] [gw3] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw1] [ 5%] PASSED tests/test_binary.py::test_overlap[same] tests/test_binary.py::test_overlap[opposite] [gw0] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] [gw2] [ 5%] PASSED tests/test_binary.py::test_join[same] tests/test_binary.py::test_join[opposite] [gw3] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] [gw0] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] [gw3] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] [gw0] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] [gw3] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] [gw1] [ 6%] PASSED tests/test_binary.py::test_overlap[opposite] tests/test_binary.py::test_intersect[False] [gw2] [ 6%] PASSED tests/test_binary.py::test_join[opposite] tests/test_binary.py::test_reldist [gw0] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] [gw3] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] [gw3] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] [gw0] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] [gw1] [ 7%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_intersect[same] [gw2] [ 7%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw3] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] [gw0] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] [gw3] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] [gw2] [ 8%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw0] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] [gw3] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] [gw2] [ 9%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw1] [ 9%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw2] [ 9%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] [gw0] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] [gw3] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] [gw0] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] [gw2] [ 10%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw3] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] [gw0] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] [gw2] [ 10%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw0] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] [gw1] [ 11%] PASSED tests/test_binary.py::test_intersect[opposite] tests/test_binary.py::test_coverage[False] [gw3] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] [gw0] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] [gw2] [ 11%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw1] [ 12%] FAILED tests/test_binary.py::test_coverage[False] tests/test_binary.py::test_coverage[same] [gw0] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] [gw3] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] [gw2] [ 12%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] tests/test_binary.py::test_k_nearest[upstream-False-same-last] [gw1] [ 12%] FAILED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_coverage[opposite] [gw0] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] [gw3] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] [gw2] [ 13%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw1] [ 13%] FAILED tests/test_binary.py::test_coverage[opposite] tests/test_binary.py::test_subtraction[same] [gw3] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] [gw0] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] [gw1] [ 14%] FAILED tests/test_binary.py::test_subtraction[same] tests/test_binary.py::test_subtraction[opposite] [gw2] [ 14%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw3] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] [gw0] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] [gw1] [ 14%] FAILED tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_subtraction[False] [gw2] [ 15%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_binary.py::test_k_nearest[upstream-True-same-last] [gw3] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] [gw0] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] [gw1] [ 15%] FAILED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw3] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] [gw2] [ 16%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw0] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] [gw2] [ 16%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw1] [ 16%] FAILED tests/test_binary.py::test_nearest[None-True-False] tests/test_binary.py::test_nearest[None-True-same] [gw3] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] [gw0] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] [gw2] [ 17%] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] tests/test_binary.py::test_k_nearest[None-False-same-last] [gw1] [ 17%] FAILED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw3] [ 17%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] [gw2] [ 17%] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] tests/test_binary.py::test_k_nearest[None-False-False-last] [gw0] [ 17%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] [gw2] [ 18%] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw1] [ 18%] FAILED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw3] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] [gw0] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw1] [ 18%] FAILED tests/test_binary.py::test_nearest[None-False-False] tests/test_binary.py::test_nearest[None-False-same] [gw2] [ 19%] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] tests/test_binary.py::test_k_nearest[None-True-same-last] [gw1] [ 19%] FAILED tests/test_binary.py::test_nearest[None-False-same] tests/test_binary.py::test_nearest[None-False-opposite] [gw3] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] [gw2] [ 19%] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] tests/test_binary.py::test_k_nearest[None-True-False-last] [gw0] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] [gw0] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] [gw2] [ 20%] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw1] [ 20%] FAILED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_nearest[upstream-True-False] [gw3] [ 20%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] [gw2] [ 20%] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest tests/test_change_chromosome_custom.py::test_change_chromosomes [gw2] [ 20%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw2] [ 21%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw2] [ 21%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_concat.py::test_concat_unstranded_stranded [gw2] [ 21%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw2] [ 21%] PASSED tests/test_count_overlaps.py::test_strand_vs_strand_same tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw0] [ 21%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] [gw1] [ 22%] FAILED tests/test_binary.py::test_nearest[upstream-True-False] tests/test_binary.py::test_nearest[upstream-True-same] [gw0] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] [gw3] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] [gw3] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] [gw2] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] [gw2] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] [gw1] [ 23%] FAILED tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw0] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] [gw3] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] [gw2] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] [gw2] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] [gw1] [ 24%] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw3] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] [gw0] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] [gw0] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] [gw2] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] [gw1] [ 25%] FAILED tests/test_binary.py::test_nearest[upstream-False-False] tests/test_binary.py::test_nearest[upstream-False-same] [gw3] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] [gw0] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] [gw0] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] [gw3] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] [gw1] [ 25%] FAILED tests/test_binary.py::test_nearest[upstream-False-same] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw2] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] [gw3] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] [gw0] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] [gw1] [ 26%] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] tests/test_binary.py::test_nearest[downstream-True-False] [gw2] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] [gw3] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] [gw1] [ 27%] FAILED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_binary.py::test_nearest[downstream-True-same] [gw2] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] [gw0] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] [gw3] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] [gw1] [ 28%] FAILED tests/test_binary.py::test_nearest[downstream-True-same] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw3] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] [gw0] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] [gw2] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] [gw1] [ 28%] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw0] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] [gw3] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] [gw2] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] [gw1] [ 29%] FAILED tests/test_binary.py::test_nearest[downstream-False-False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] [gw3] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] [gw0] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] [gw2] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] [gw1] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw3] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw1] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] [gw3] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] [gw0] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] [gw2] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] [gw1] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] [gw3] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] [gw0] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] [gw2] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] [gw1] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] [gw2] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] [gw3] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] [gw0] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] [gw1] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] [gw2] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] [gw2] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] [gw3] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] [gw0] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] [gw1] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] [gw0] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] [gw0] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] [gw3] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] [gw2] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] [gw0] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] [gw1] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] [gw2] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] [gw0] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw3] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] [gw0] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw1] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] [gw2] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] [gw3] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] [gw0] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] [gw1] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] [gw2] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] [gw1] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] [gw0] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] [gw3] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw2] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] [gw1] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] [gw0] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw3] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] [gw2] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] [gw1] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] [gw3] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] [gw0] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] [gw2] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] [gw3] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] [gw3] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] [gw3] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] [gw1] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] [gw0] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] [gw2] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] [gw3] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] [gw1] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] [gw3] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] [gw0] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] [gw2] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] [gw1] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] [gw3] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] [gw0] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] [gw2] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] [gw1] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] [gw3] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] [gw0] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] [gw2] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] [gw1] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] [gw3] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] [gw2] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] [gw2] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] [gw2] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] [gw1] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] [gw3] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] [gw1] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] [gw0] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] [gw1] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] [gw0] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] [gw1] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] [gw2] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] [gw2] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] [gw3] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] [gw2] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw0] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] [gw1] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] [gw0] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] [gw1] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] [gw2] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] [gw3] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] [gw0] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] [gw0] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] [gw1] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] [gw2] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] [gw3] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] [gw0] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] [gw1] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] [gw2] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] [gw3] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] [gw0] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] [gw2] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] [gw1] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] [gw3] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] [gw0] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] [gw3] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] [gw2] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] [gw1] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] [gw2] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw0] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] [gw3] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] [gw1] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] [gw3] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] [gw3] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] [gw3] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] [gw2] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] [gw0] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] [gw1] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] [gw3] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw2] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] [gw0] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw3] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] [gw1] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] [gw2] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] [gw0] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] [gw3] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] [gw2] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] [gw0] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] [gw3] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] [gw1] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] [gw2] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] [gw0] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] [gw3] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] [gw1] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] [gw1] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] [gw2] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] [gw0] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] [gw3] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] [gw1] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] [gw2] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] [gw0] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] [gw1] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] [gw3] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] [gw2] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] [gw0] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] [gw1] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] [gw3] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] [gw2] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] [gw2] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] [gw0] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] [gw1] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] [gw3] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] [gw0] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] [gw2] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] [gw1] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] [gw2] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] [gw0] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] [gw3] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] [gw2] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] [gw1] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] [gw2] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw0] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] [gw3] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] [gw0] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] [gw3] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] [gw2] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] [gw1] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] [gw0] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] [gw2] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] [gw3] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] [gw0] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] [gw3] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] [gw1] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] [gw2] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] [gw0] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] [gw3] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] [gw0] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] [gw3] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] [gw1] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] [gw1] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] [gw2] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] [gw2] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] [gw3] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] [gw0] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] [gw1] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] [gw1] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw2] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] [gw3] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] [gw0] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] [gw2] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] [gw1] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] [gw1] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] [gw3] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] [gw2] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] [gw0] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] [gw2] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] [gw3] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] [gw1] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] [gw0] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw2] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] [gw3] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] [gw1] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] [gw3] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] [gw1] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] [gw0] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] [gw2] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] [gw3] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] [gw1] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] [gw2] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] [gw0] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw3] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] [gw1] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] [gw3] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] [gw1] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] [gw0] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] [gw2] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] [gw3] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] [gw1] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] [gw0] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] [gw2] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] [gw3] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] [gw1] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] [gw1] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] [gw1] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] [gw1] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] [gw2] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] [gw0] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] [gw0] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] [gw3] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] [gw2] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] [gw1] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] [gw1] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] [gw0] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] [gw0] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] [gw2] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] [gw3] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] [gw3] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] [gw1] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] [gw2] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] [gw0] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] [gw0] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] [gw1] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] [gw3] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] [gw2] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] [gw3] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] [gw1] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] [gw0] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] [gw3] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] [gw2] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] [gw3] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] [gw1] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] [gw0] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw3] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] [gw2] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] [gw1] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] [gw2] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] [gw0] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] [gw3] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] [gw1] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] [gw2] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] [gw1] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] [gw2] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] [gw3] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] [gw0] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] [gw1] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] [gw2] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] [gw2] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] [gw3] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] [gw0] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] [gw1] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] [gw2] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] [gw3] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] [gw1] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] [gw1] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] [gw0] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] [gw1] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] [gw3] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] [gw2] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] [gw2] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] [gw0] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] [gw0] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] [gw1] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] [gw3] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] [gw2] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] [gw0] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] [gw2] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] [gw0] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] [gw1] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] [gw3] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw2] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] [gw0] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] [gw2] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] [gw3] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] [gw1] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] [gw0] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] [gw2] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] [gw3] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] [gw0] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] [gw1] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] [gw2] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] [gw3] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] [gw0] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] [gw2] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] [gw3] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] [gw2] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] [gw1] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] [gw2] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] [gw0] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] [gw3] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] [gw1] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] [gw2] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] [gw0] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] [gw2] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] [gw3] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] [gw0] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] [gw1] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] [gw2] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] [gw3] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] [gw0] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] [gw3] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] [gw1] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] [gw2] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] [gw2] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] [gw0] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] [gw3] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] [gw1] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] [gw0] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] [gw2] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] [gw3] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] [gw2] [ 91%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] [gw1] [ 92%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] [gw1] [ 92%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] [gw1] [ 92%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] [gw3] [ 92%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] [gw2] [ 92%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] [gw0] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] [gw1] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] [gw1] [ 93%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] [gw2] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] [gw0] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] [gw3] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] [gw1] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] [gw2] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] [gw1] [ 94%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] tests/test_getset_attr.py::test_getsetattr_fails [gw1] [ 94%] PASSED tests/test_getset_attr.py::test_getsetattr_fails tests/test_io.py::test_read_gtf [gw1] [ 94%] PASSED tests/test_io.py::test_read_gtf tests/test_io.py::test_read_gff3 [gw1] [ 95%] PASSED tests/test_io.py::test_read_gff3 tests/test_io.py::test_read_bed [gw1] [ 95%] PASSED tests/test_io.py::test_read_bed tests/test_pickle.py::test_pickle [gw1] [ 95%] PASSED tests/test_pickle.py::test_pickle tests/test_stranded.py::test_stranded [gw1] [ 95%] PASSED tests/test_stranded.py::test_stranded tests/test_stranded.py::test_unstrand [gw1] [ 95%] PASSED tests/test_stranded.py::test_unstrand tests/test_unary.py::test_merge[True] [gw2] [ 96%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] tests/test_getset_attr.py::test_getsetattr_with_str [gw2] [ 96%] PASSED tests/test_getset_attr.py::test_getsetattr_with_str tests/test_unary.py::test_cluster[True] [gw3] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw0] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] tests/test_genomicfeatures.py::test_introns_single [gw0] [ 96%] FAILED tests/test_genomicfeatures.py::test_introns_single tests/test_getset_attr.py::test_getsetattr [gw0] [ 96%] PASSED tests/test_getset_attr.py::test_getsetattr tests/test_unary.py::test_cluster_by[False] [gw1] [ 97%] FAILED tests/test_unary.py::test_merge[True] tests/test_unary.py::test_merge[False] [gw2] [ 97%] FAILED tests/test_unary.py::test_cluster[True] tests/test_unary.py::test_cluster[False] [gw1] [ 97%] FAILED tests/test_unary.py::test_merge[False] tests/test_unary.py::test_merge_by[False] [gw3] [ 97%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] tests/test_unary.py::test_cluster_by[True] [gw2] [ 97%] FAILED tests/test_unary.py::test_cluster[False] tests/test_unary.py::test_windows [gw2] [ 98%] FAILED tests/test_unary.py::test_windows tests/test_unary.py::test_getitem [gw2] [ 98%] PASSED tests/test_unary.py::test_getitem tests/test_unary.py::test_summary [gw2] [ 98%] FAILED tests/test_unary.py::test_summary tests/windows/test_windows.py::test_windows [gw2] [ 98%] FAILED tests/windows/test_windows.py::test_windows tests/windows/test_windows.py::test_windows2 [gw2] [ 98%] FAILED tests/windows/test_windows.py::test_windows2 [gw1] [ 99%] PASSED tests/test_unary.py::test_merge_by[False] tests/test_unary.py::test_init[True] [gw1] [ 99%] PASSED tests/test_unary.py::test_init[True] [gw3] [ 99%] PASSED tests/test_unary.py::test_cluster_by[True] tests/test_unary.py::test_init[False] [gw0] [ 99%] PASSED tests/test_unary.py::test_cluster_by[False] tests/test_unary.py::test_merge_by[True] [gw3] [ 99%] PASSED tests/test_unary.py::test_init[False] [gw0] [100%] PASSED tests/test_unary.py::test_merge_by[True] =================================== FAILURES =================================== ____________ test_three_in_a_row[strandedness_chain1-method_chain1] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain35-method_chain35] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 127 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________________________ test_set_intersect[False] ___________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:128: in test_set_intersect result = gr.set_intersect(gr2, strandedness=strandedness) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_intersect( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8mc35jmn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8mc35jmn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5gx9pkk5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5gx9pkk5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps9mnttgy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps9mnttgy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpteyf6ylv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpteyf6ylv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxgpkecsh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxgpkecsh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa8zjufr6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa8zjufr6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo9da4pcj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo9da4pcj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprrcfmogx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprrcfmogx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuoeof3xb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuoeof3xb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk5v689iw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk5v689iw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzco76zn3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzco76zn3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6dr7kcao/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6dr7kcao/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpidnzlbtt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpidnzlbtt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2hznx0k6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2hznx0k6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6gig4zbh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6gig4zbh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphc60_wu4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphc60_wu4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8m17hy67/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8m17hy67/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcuph11ai/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcuph11ai/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmparlf5op7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmparlf5op7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw0ir5x46/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw0ir5x46/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsscmax8f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsscmax8f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpicifjmm0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpicifjmm0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_v5dqy0q/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_v5dqy0q/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmproepzglt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmproepzglt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpn9diyy5k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn9diyy5k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgh47tdc2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgh47tdc2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps244lg72/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps244lg72/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1pwbzkii/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1pwbzkii/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoyh2uwam/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoyh2uwam/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnn83pc09/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnn83pc09/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxxobhwx1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxxobhwx1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2a0092zy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2a0092zy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpb3k9msi3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb3k9msi3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphzqxdtah/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphzqxdtah/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5xqqqohx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5xqqqohx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7x7lfu2d/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7x7lfu2d/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpibx2mv2k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpibx2mv2k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp55vzthdj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp55vzthdj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoa2avdca/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoa2avdca/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaz2kv1rz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaz2kv1rz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzc8hbeve/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzc8hbeve/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprkkbobg_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprkkbobg_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpja95bh_t/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpja95bh_t/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp25nhv3h_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp25nhv3h_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3qolc2ak/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3qolc2ak/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppkswcxpn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppkswcxpn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpr4gusi9q/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr4gusi9q/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0vpaygch/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0vpaygch/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpc90t8nw1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc90t8nw1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5z2x06m3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5z2x06m3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpq5hct2s7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq5hct2s7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpckbrkyza/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpckbrkyza/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0w8s6ohe/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0w8s6ohe/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuq9uk9lo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuq9uk9lo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpr3h2f_ou/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr3h2f_ou/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpayieslt9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpayieslt9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp___6eohm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp___6eohm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjrslxxc3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjrslxxc3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0futkuc1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0futkuc1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsa_apauv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsa_apauv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppnmkyiex/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppnmkyiex/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpglmddwzb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpglmddwzb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2sub_frh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2sub_frh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm187tmfg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm187tmfg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp52ud6qf1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp52ud6qf1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1yj8bycm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1yj8bycm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5bd5m8fz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5bd5m8fz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmqrbrwm0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmqrbrwm0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpblzm207s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpblzm207s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnip0o35c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnip0o35c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp04zcki7o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp04zcki7o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp33tp51o_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp33tp51o_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7pokcuuj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7pokcuuj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppmo_b8jc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppmo_b8jc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph47mzks7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph47mzks7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcogxzh0x/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcogxzh0x/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpudvk1br9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpudvk1br9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpc7zo7w68/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc7zo7w68/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpndre734w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpndre734w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdo2_fvab/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdo2_fvab/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptmgcv7rs/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptmgcv7rs/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp35stvq2y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp35stvq2y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3cqb4qwy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3cqb4qwy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpma6ds3sm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpma6ds3sm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqzuyy87g/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqzuyy87g/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjc8esye_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjc8esye_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo4mdfpzr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo4mdfpzr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpus4cctmi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpus4cctmi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuqhhus8l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuqhhus8l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf0qfmrhc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf0qfmrhc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpb6dpki_k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb6dpki_k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjndsjtpi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjndsjtpi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3e99ykvv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3e99ykvv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7qlk5hrq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7qlk5hrq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpipj4n3dz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpipj4n3dz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpt55acq5b/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt55acq5b/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgydy3jt8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgydy3jt8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp83jmr551/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp83jmr551/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprhmxr4xy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprhmxr4xy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfzvlayel/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfzvlayel/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsvouw1ml/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsvouw1ml/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpag1swhbu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpag1swhbu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvlm4e52h/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvlm4e52h/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp62d27o0f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp62d27o0f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpud87khge/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpud87khge/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx_jrkm0f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx_jrkm0f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm3ool7v6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm3ool7v6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe3tovidq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe3tovidq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpiuve5810/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiuve5810/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdvl2tpp3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdvl2tpp3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphm2bd_2g/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphm2bd_2g/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8w7wa53j/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8w7wa53j/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1h5mc97v/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1h5mc97v/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpukh3got8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpukh3got8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8bhheqf8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8bhheqf8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpd_mm7k2f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd_mm7k2f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp2ftg_s6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp2ftg_s6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1d_rkdy0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1d_rkdy0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppwca3up9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppwca3up9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9x2arb5i/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9x2arb5i/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvpdk_l58/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvpdk_l58/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe8ohknv8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe8ohknv8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcxs0fv8y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcxs0fv8y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsjy71elf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsjy71elf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx9kztsqx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx9kztsqx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0aimppic/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0aimppic/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnj_1sprh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnj_1sprh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgnltvq7o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgnltvq7o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4by85xol/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4by85xol/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpi1ns8wpi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi1ns8wpi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe0htt3zp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe0htt3zp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzc1a5yz7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzc1a5yz7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplgmiwk_u/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplgmiwk_u/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp02q6_mto/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp02q6_mto/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptzvtbjz4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptzvtbjz4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwzq1a0pc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwzq1a0pc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9gfbek9y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9gfbek9y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsud0_0e2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsud0_0e2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl0sk6lar/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl0sk6lar/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpge_7vagm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpge_7vagm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpouwq954m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpouwq954m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgq8c0dzk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgq8c0dzk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps8nn0cfr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps8nn0cfr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbh4e2rds/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbh4e2rds/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp07n136dd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp07n136dd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2efowe1h/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2efowe1h/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp92wfs7q8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp92wfs7q8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7hw6toh9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7hw6toh9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpr2jd5fmb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr2jd5fmb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvsud7qkb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvsud7qkb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpokgy9eld/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpokgy9eld/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbny0qrut/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbny0qrut/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe49uyrjk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe49uyrjk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvktzzo9w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvktzzo9w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfb7atdq3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfb7atdq3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcyk77uf7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcyk77uf7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2xx082wr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2xx082wr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgmf4nxo1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgmf4nxo1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgzbol48x/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgzbol48x/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7jrll6a5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7jrll6a5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjws52f5x/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjws52f5x/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7v58jpkq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7v58jpkq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoqevnplv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoqevnplv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppzsid0bb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppzsid0bb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpq1b9ztk9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq1b9ztk9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdvitm5od/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdvitm5od/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxbxzhl_8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxbxzhl_8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8jx389dj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8jx389dj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvkqsjiey/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvkqsjiey/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl1fz0o4a/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl1fz0o4a/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx_o51mar/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx_o51mar/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptj6l4w75/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptj6l4w75/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpz84_d7qs/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz84_d7qs/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxflr9uz9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxflr9uz9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprkt4t9bm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprkt4t9bm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpibbl7gl2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpibbl7gl2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4oko4d4o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4oko4d4o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0g2z2zj8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0g2z2zj8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkp6_rtdo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkp6_rtdo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuo_t9se1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuo_t9se1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgf0jiimq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgf0jiimq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph1jjibr_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph1jjibr_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpebgdi7ch/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpebgdi7ch/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgn783gwj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgn783gwj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpja3sy9rw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpja3sy9rw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7ioqxcsa/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7ioqxcsa/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv5wlsp5d/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv5wlsp5d/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnvadjn51/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnvadjn51/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpd9fnj1dx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd9fnj1dx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxc1qehu9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxc1qehu9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkdf847ou/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkdf847ou/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaq0qsyax/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaq0qsyax/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgscz8jei/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgscz8jei/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp34f35qvr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp34f35qvr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyi25ysfi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyi25ysfi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp26skmzcp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp26skmzcp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7km92598/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7km92598/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqjq8vwks/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqjq8vwks/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbmk1rowj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbmk1rowj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3f6ptc2l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3f6ptc2l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcvot5gzk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcvot5gzk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbvwmz9mr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbvwmz9mr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_qt7q51e/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_qt7q51e/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphxa1num4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphxa1num4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxzbevl3y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxzbevl3y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbmxbenjc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbmxbenjc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnbregoqn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnbregoqn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmb3cmzrp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmb3cmzrp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp85ah2ie3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp85ah2ie3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpiqm_2yel/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiqm_2yel/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5qwpp4o2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5qwpp4o2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjs8xasmd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjs8xasmd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphbjy5hci/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphbjy5hci/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa5mzvzkz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa5mzvzkz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpj853hgtr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj853hgtr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4aokcekq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4aokcekq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp07krkmo3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp07krkmo3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqku835zf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqku835zf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw81xg5jq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw81xg5jq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaqnaed3b/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaqnaed3b/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqd2ma_lo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqd2ma_lo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx9iidxz4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx9iidxz4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp71kkkl3l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp71kkkl3l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpec359bbt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpec359bbt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwy48q96w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwy48q96w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpws5optpf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpws5optpf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcbxovhnc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcbxovhnc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0jwqsrsa/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0jwqsrsa/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf7_pdoj0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf7_pdoj0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpywai6urd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpywai6urd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmykv334x/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmykv334x/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpr5hk_oof/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr5hk_oof/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo2yxmi8p/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo2yxmi8p/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5l6_40ec/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5l6_40ec/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp46w54_oz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp46w54_oz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyixttsmq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyixttsmq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjysxr2r6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjysxr2r6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_nearest[downstream-False-same] ______________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 513 | 770 | a | 0 | - | | | chr1 | 266 | 523 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 265480 | 265738 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RkZWBkzGMAAUZGBmYGJiAlz8DICeKDhMSYpJjBTBZediCXkYERAB+8AP8=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp61gox1bz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61gox1bz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7526046y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7526046y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbw3c1sa5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbw3c1sa5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpydvmxjv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydvmxjv8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxpaw6sr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxpaw6sr0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4yia6i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4yia6i1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzsptv6wd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzsptv6wd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuet2dcvv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuet2dcvv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo8r4h_x3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo8r4h_x3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy6fep53i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6fep53i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyo3rkn4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyo3rkn4o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcalfivq3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcalfivq3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg5fncj0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5fncj0_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqpthkwj6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqpthkwj6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3y7r_fn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3y7r_fn0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprutzc0yy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprutzc0yy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeys0frvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeys0frvi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp15l_fb89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15l_fb89/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2_5_jibg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2_5_jibg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8oio8tqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8oio8tqm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1zuz7aey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zuz7aey/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphm9qyf5r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphm9qyf5r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg51eidcc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg51eidcc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_as6famt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_as6famt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdrr4wlur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrr4wlur/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9dd0gl9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9dd0gl9u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp74_kdwvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74_kdwvh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx52ocof9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx52ocof9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj1j77jgq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1j77jgq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_6fk7s6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6fk7s6d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjq4_3dpo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjq4_3dpo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz8g6sshl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8g6sshl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxqirc879/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqirc879/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmrdrs82a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmrdrs82a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1h8fgjai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1h8fgjai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2zly__0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zly__0d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7quw0uot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7quw0uot/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp75jsevmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75jsevmv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnop42kap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnop42kap/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyvlfume5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvlfume5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmnqvp66l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmnqvp66l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzogel8o8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzogel8o8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp28__ef4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28__ef4e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd4y8zti8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd4y8zti8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptnts1mup/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptnts1mup/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcpvak51w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcpvak51w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw5_jwdwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5_jwdwy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkdvskqem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdvskqem/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptmcm7x4f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptmcm7x4f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1sg0xvg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sg0xvg5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplocmyx95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplocmyx95/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdznd7z7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdznd7z7q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsqvnhww_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqvnhww_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_xszk8zv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_xszk8zv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5d01j4ol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5d01j4ol/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2uo8kkr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uo8kkr3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe90_esv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe90_esv_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph6gsobta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6gsobta/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi2t98snh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2t98snh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphffnvo5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphffnvo5q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgdhqtgty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdhqtgty/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9085ew47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9085ew47/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyy2hw55d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyy2hw55d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpanvvkjo6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpanvvkjo6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4tk868fh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tk868fh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmk5z5h89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk5z5h89/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy_m9i6l0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_m9i6l0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpskwa9bmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskwa9bmi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsbhhtqjt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbhhtqjt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp3ouglvo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp3ouglvo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb8tewhed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb8tewhed/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz41nocwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz41nocwk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj3l1_zd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3l1_zd2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpav7f8a9q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpav7f8a9q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvrags3m9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrags3m9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk1wgv_md/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1wgv_md/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0z5x79mj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0z5x79mj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsat3uc0z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsat3uc0z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp665e8mpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp665e8mpk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3x9cc8z5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3x9cc8z5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_5i_c8_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5i_c8_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1v4dwc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1v4dwc5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqh50q51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqh50q51/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyz0buwnt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyz0buwnt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv8b8pewp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv8b8pewp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7zm666zi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7zm666zi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpojd21z67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpojd21z67/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp29vxqffd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp29vxqffd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6f4w0fcc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6f4w0fcc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7fl139bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fl139bk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1hr9n1wi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1hr9n1wi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc_3kows1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_3kows1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuo3xhq_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuo3xhq_g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp464o9yf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp464o9yf6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpddfoogvv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpddfoogvv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvkx1mwzl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkx1mwzl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt4lmuak0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4lmuak0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmqxw6kqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqxw6kqd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpewuwp13s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpewuwp13s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeg1irk2g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeg1irk2g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpra38metf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpra38metf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9iprg7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9iprg7o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiab65knm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiab65knm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7j8iv4s9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7j8iv4s9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwzh58w0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwzh58w0e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphmpl3fwu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmpl3fwu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp59i59kfk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59i59kfk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph2l90wyc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2l90wyc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzvs46occ/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvs46occ/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbey6xqtr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbey6xqtr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6jz79_xh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6jz79_xh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm_0y5cts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_0y5cts/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsg85mwoi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsg85mwoi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo6_2dcx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6_2dcx5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8cx17r1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8cx17r1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp98mx3kl2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98mx3kl2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdxkdk1_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxkdk1_s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg15sipyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg15sipyp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4qkghy1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4qkghy1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa_xp4yyg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_xp4yyg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_6nzen0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6nzen0b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplt667hu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplt667hu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcfeb_gau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcfeb_gau/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq7lesfn4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq7lesfn4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwv2y5op5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwv2y5op5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi32o8ei3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi32o8ei3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7bge7bhp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bge7bhp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkhfa6rn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkhfa6rn8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkagnqvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkagnqvk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_phanxvn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_phanxvn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw611rsml/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw611rsml/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfrpupygu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfrpupygu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvns2gmkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvns2gmkm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2sbgcx_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2sbgcx_o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzyb8jr5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyb8jr5_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7eaou31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7eaou31/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3dhv2mh4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dhv2mh4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp62k52lmd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62k52lmd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi15wmrkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi15wmrkl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpus8pncwc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpus8pncwc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8834k0mf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8834k0mf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp33g9j8rg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33g9j8rg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5lavtxq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5lavtxq4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqgxfhk9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqgxfhk9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphnlrlvdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphnlrlvdo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9694ze31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9694ze31/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv49ynguh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv49ynguh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppjwtyper/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjwtyper/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain2-method_chain2] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ___________ test_three_in_a_row[strandedness_chain36-method_chain36] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E (and 120 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________________ test_set_intersect[same] ___________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:128: in test_set_intersect result = gr.set_intersect(gr2, strandedness=strandedness) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_intersect( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvcs4uh62/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvcs4uh62/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpr3c7bykt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr3c7bykt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbd9su3fy/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbd9su3fy/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcl82gvm1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcl82gvm1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3thrsend/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3thrsend/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvbqiwh44/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvbqiwh44/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqced_i4s/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqced_i4s/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppkdb66bm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppkdb66bm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpoockudw3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoockudw3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2ni7vate/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2ni7vate/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplv7wuezw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplv7wuezw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6uypt5n2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6uypt5n2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4a6napy3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4a6napy3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplo4rymuk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplo4rymuk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwhy1wyui/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwhy1wyui/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9jlm0rq_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9jlm0rq_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo5j1kqxf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo5j1kqxf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4gakr3db/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4gakr3db/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplx746_fb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplx746_fb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptmknprpd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptmknprpd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4wf_nwp3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4wf_nwp3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_d0i6lp6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_d0i6lp6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcp4x7n13/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcp4x7n13/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplya8dtxl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplya8dtxl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9pga9myo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9pga9myo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7dd36k3w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7dd36k3w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk7pla5ee/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk7pla5ee/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnp4ym9mb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnp4ym9mb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpli03yhco/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpli03yhco/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfqleizj9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfqleizj9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8a1mjnf5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8a1mjnf5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6ywj97dm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6ywj97dm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm7nqujmf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm7nqujmf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9www3cd8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9www3cd8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp20s9_iep/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp20s9_iep/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpde3b4rqb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpde3b4rqb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzi0t5xun/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzi0t5xun/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5ek_9u7m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5ek_9u7m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpde8w_kg2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpde8w_kg2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0_1z_k1q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0_1z_k1q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph7x1hipi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph7x1hipi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjyz1k6j1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjyz1k6j1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsmj6a1zn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsmj6a1zn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp11yiq7hp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp11yiq7hp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpeeefcvdt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeeefcvdt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfxelmjir/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfxelmjir/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpodrg4glg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpodrg4glg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpac49fww3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpac49fww3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0qjzgzf8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0qjzgzf8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7fnh2jrf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7fnh2jrf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgdtz_yfa/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgdtz_yfa/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp26255xs5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp26255xs5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_in2hkt8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_in2hkt8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp61wgqn_0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp61wgqn_0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphmn0eplk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphmn0eplk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvrn0szyp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvrn0szyp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2pd_9ejl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2pd_9ejl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzlp84f7e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzlp84f7e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbqh70lsc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbqh70lsc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9sml8wl1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9sml8wl1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqoxo0hz1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqoxo0hz1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6v7jr0fu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6v7jr0fu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnjkydct5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnjkydct5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzqnsllr4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzqnsllr4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph_7woqow/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph_7woqow/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk0r57j0x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk0r57j0x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpla0s3tun/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpla0s3tun/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqtrfl8w8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqtrfl8w8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphtxl_65a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphtxl_65a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgezikk87/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgezikk87/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp71tck7e6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp71tck7e6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqescig0z/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqescig0z/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2jpz42a9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2jpz42a9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8hqah7km/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8hqah7km/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpj9xaw0jz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj9xaw0jz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxnrchtfu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxnrchtfu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfm9m4rfx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfm9m4rfx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpps30tufn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpps30tufn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpa4ytwsq9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa4ytwsq9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpn8r48f32/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn8r48f32/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfeaa6yxi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfeaa6yxi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1j1jk8x9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1j1jk8x9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1r8c19jx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1r8c19jx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkaetj7_i/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkaetj7_i/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6b9coru1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6b9coru1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpeqso37ij/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeqso37ij/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphnmvhf1x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphnmvhf1x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8kiw_4la/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8kiw_4la/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnh_c0fa3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnh_c0fa3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphmix7ctw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphmix7ctw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4swzignv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4swzignv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7k3ncpea/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7k3ncpea/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdcfhnj1o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdcfhnj1o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpn14xicjz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn14xicjz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph3yji23d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph3yji23d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8hizgic4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8hizgic4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp50ya9nps/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp50ya9nps/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpng5htcf1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpng5htcf1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjfeg2i8d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjfeg2i8d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnvw8ncom/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnvw8ncom/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp30sukted/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp30sukted/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo07850dn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo07850dn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp64j2sdxy/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp64j2sdxy/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpoketa383/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoketa383/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsj0_ri_e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsj0_ri_e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp773rv4xg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp773rv4xg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7su2nrwr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7su2nrwr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc9zywei0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc9zywei0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3gq56g3q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3gq56g3q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7lykx2rb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7lykx2rb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx_kgchz3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx_kgchz3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphca06p8w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphca06p8w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvkplh74w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvkplh74w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcbikv3cx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcbikv3cx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqp392f5b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqp392f5b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpn2qdh23w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn2qdh23w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfly7frma/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfly7frma/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpri8gho9t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpri8gho9t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4uksn4kc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4uksn4kc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjayfm486/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjayfm486/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqt3gkn8i/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqt3gkn8i/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy5dfa_dr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy5dfa_dr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpel9flp5l/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpel9flp5l/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7j6trq6r/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7j6trq6r/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmy71aelz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmy71aelz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8hf0v7gw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8hf0v7gw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphr5nz6f3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphr5nz6f3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4soiov0g/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4soiov0g/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp1l4qis9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp1l4qis9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdt1fhhoc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdt1fhhoc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgajjuo4o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgajjuo4o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphg266w6d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphg266w6d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpunrdy6ac/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpunrdy6ac/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_nearest[downstream-False-opposite] ____________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 4483616 | 4486938 | a | 0 | + | | | chr1 | 4465478 | 4468800 | a | 0 | + | | | chr1 | 9769723 | 9773045 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 3163 | 3176 | a | 0 | + | | | chr18 | 3163 | 3478 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAEA3LVh0wlBA3k2BGWHDIoHBByZEuHicoQ0m2oADQEBEwERAgEXAR4AAQAHAF9Eah8RAwJ4lRL6ABlEI0UfDlQxkQz5BgEAEgMCARACGwIAAAF7AAAABFc7jh8ABwEBAAARAAwADFoBAQsADAACAToMAQACAAEA') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 27152 | 27187 | a | 0 | + | | | chr1 | 27152 | 27921 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 315 | 316 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QwmZ3FyM7Cxc7AwAiEWfzMQFKJgYGZASQQbt0HooDYioEHRAEAYw4DZg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2dmkx5mq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dmkx5mq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0k17zz6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0k17zz6b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyc1i1pr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyc1i1pr3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt6aug14w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6aug14w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvoc3yhor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvoc3yhor/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_48itee7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_48itee7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj1i6pnpc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1i6pnpc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf_7wu668/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_7wu668/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5l6kg702/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5l6kg702/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp87v3o_pe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87v3o_pe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpup1l7kkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpup1l7kkv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpul05qlmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpul05qlmh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_tsj408o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tsj408o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxu7qbizs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxu7qbizs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjqkolpfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqkolpfu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprn_8hdr7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprn_8hdr7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwowxtipm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwowxtipm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ti945fc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ti945fc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0pob_j4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0pob_j4m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_i1bl33g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i1bl33g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3g97yifp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3g97yifp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3i0ljal0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3i0ljal0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnno0z16i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnno0z16i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpog2x06ft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpog2x06ft/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp70e53wa0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70e53wa0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqda62hkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqda62hkx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz07mrb7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz07mrb7o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpieoc_n1x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpieoc_n1x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9u9f1u4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9u9f1u4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp07gsmir6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07gsmir6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5dse10me/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5dse10me/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcansetts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcansetts/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxrrypxsa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrrypxsa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4nzgnys7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4nzgnys7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4czu59em/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4czu59em/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr0zy_m79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0zy_m79/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuj5dc7vv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuj5dc7vv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuyv1eh72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyv1eh72/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjkee_5rm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjkee_5rm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_u6o8quk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_u6o8quk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyfm19und/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfm19und/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu0fdknv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0fdknv2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ads5a3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ads5a3c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjrzxdfoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjrzxdfoz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy2bhzlx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2bhzlx5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsnlqu7sj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsnlqu7sj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpabiljztn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabiljztn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp783vpcs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp783vpcs5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9xlcw4yx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xlcw4yx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsz07r2z7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsz07r2z7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcgj5ugtl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgj5ugtl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5208rmro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5208rmro/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu8flohcz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8flohcz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp7gq7wm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7gq7wm3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpii1aaem4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpii1aaem4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppx5dhvmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppx5dhvmv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv_4_k7w4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_4_k7w4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplluwugl4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplluwugl4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsmm7rjgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsmm7rjgg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy4c2bm89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4c2bm89/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsi1dyiz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsi1dyiz4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo2d091te/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2d091te/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpigsiowc2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigsiowc2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpao8xi_qp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpao8xi_qp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp7q24084/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7q24084/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm8x7ntpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8x7ntpl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6xuopfys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xuopfys/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplrf1kupj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplrf1kupj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0b_61d24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0b_61d24/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp32b4vj4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32b4vj4z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5c581_j9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5c581_j9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp03l9h15y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03l9h15y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp62o3pc13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62o3pc13/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7mn3itd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7mn3itd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpilok7uc3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpilok7uc3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4pje6doh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pje6doh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt6d4_2h6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6d4_2h6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqdxtp5fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdxtp5fa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_28h5121/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_28h5121/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdynd23gi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdynd23gi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1dbft1jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1dbft1jl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwnuquyn9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwnuquyn9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyfdxaq76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfdxaq76/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr8ehoe61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8ehoe61/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvh0ufcl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvh0ufcl6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpihdoiaei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihdoiaei/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6p10acfz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6p10acfz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg8gviy3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8gviy3w/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain3-method_chain3] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 181 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain37-method_chain37] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________________ test_set_union[False] _____________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:149: in test_set_union result = gr.set_union(gr2, strandedness=strandedness) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_union( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmpe6b442dp/f1.bed /tmp/tmpe6b442dp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8kqglvwn/f1.bed /tmp/tmp8kqglvwn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbc1mh8f6/f1.bed /tmp/tmpbc1mh8f6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprijdfufa/f1.bed /tmp/tmprijdfufa/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8keh59q7/f1.bed /tmp/tmp8keh59q7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprr4tlmzy/f1.bed /tmp/tmprr4tlmzy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprqzhz9ot/f1.bed /tmp/tmprqzhz9ot/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpawa35xq0/f1.bed /tmp/tmpawa35xq0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpao3qyhkh/f1.bed /tmp/tmpao3qyhkh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprjgnl56p/f1.bed /tmp/tmprjgnl56p/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjb6op6tq/f1.bed /tmp/tmpjb6op6tq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw43zcdzz/f1.bed /tmp/tmpw43zcdzz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe5wyui5h/f1.bed /tmp/tmpe5wyui5h/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0syvnrcj/f1.bed /tmp/tmp0syvnrcj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0_x9bx6r/f1.bed /tmp/tmp0_x9bx6r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd9jhufhz/f1.bed /tmp/tmpd9jhufhz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplzvpnaw4/f1.bed /tmp/tmplzvpnaw4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3066gh15/f1.bed /tmp/tmp3066gh15/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjlkjpqlc/f1.bed /tmp/tmpjlkjpqlc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9ih3kx60/f1.bed /tmp/tmp9ih3kx60/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8eq4hrr5/f1.bed /tmp/tmp8eq4hrr5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxy5kbald/f1.bed /tmp/tmpxy5kbald/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppui965sk/f1.bed /tmp/tmppui965sk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_fut88q_/f1.bed /tmp/tmp_fut88q_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4dq3cloe/f1.bed /tmp/tmp4dq3cloe/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkw1k8hyh/f1.bed /tmp/tmpkw1k8hyh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4s67ugjd/f1.bed /tmp/tmp4s67ugjd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbq87r2sr/f1.bed /tmp/tmpbq87r2sr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0r5_2f_q/f1.bed /tmp/tmp0r5_2f_q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9mey4boq/f1.bed /tmp/tmp9mey4boq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt77rhl_2/f1.bed /tmp/tmpt77rhl_2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1l70x_vp/f1.bed /tmp/tmp1l70x_vp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqb4ivh1c/f1.bed /tmp/tmpqb4ivh1c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp907lph97/f1.bed /tmp/tmp907lph97/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppv3x241_/f1.bed /tmp/tmppv3x241_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7bzkjse7/f1.bed /tmp/tmp7bzkjse7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj6e50d3y/f1.bed /tmp/tmpj6e50d3y/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpohmur2or/f1.bed /tmp/tmpohmur2or/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8mlbm606/f1.bed /tmp/tmp8mlbm606/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8kywkmrc/f1.bed /tmp/tmp8kywkmrc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5jf_3ltj/f1.bed /tmp/tmp5jf_3ltj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp862lrajh/f1.bed /tmp/tmp862lrajh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn9ofvvmc/f1.bed /tmp/tmpn9ofvvmc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp31mo97jg/f1.bed /tmp/tmp31mo97jg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2nj8y8wd/f1.bed /tmp/tmp2nj8y8wd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdnn9dop2/f1.bed /tmp/tmpdnn9dop2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_fcbbzgd/f1.bed /tmp/tmp_fcbbzgd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe4um1vxd/f1.bed /tmp/tmpe4um1vxd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppvr_o6s0/f1.bed /tmp/tmppvr_o6s0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpck5rcou2/f1.bed /tmp/tmpck5rcou2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk1raz48w/f1.bed /tmp/tmpk1raz48w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp91z6yhzw/f1.bed /tmp/tmp91z6yhzw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw6ydbhdw/f1.bed /tmp/tmpw6ydbhdw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqg1bky19/f1.bed /tmp/tmpqg1bky19/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0nd1cpdr/f1.bed /tmp/tmp0nd1cpdr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp12_2nawt/f1.bed /tmp/tmp12_2nawt/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf1wsx9ki/f1.bed /tmp/tmpf1wsx9ki/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa723j92a/f1.bed /tmp/tmpa723j92a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp4xywy8o/f1.bed /tmp/tmpp4xywy8o/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzacyc3xx/f1.bed /tmp/tmpzacyc3xx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf_cphr5f/f1.bed /tmp/tmpf_cphr5f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwb09vypg/f1.bed /tmp/tmpwb09vypg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptpd8bvkk/f1.bed /tmp/tmptpd8bvkk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvokgbc9l/f1.bed /tmp/tmpvokgbc9l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbbgk5n0d/f1.bed /tmp/tmpbbgk5n0d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx6i1e7r2/f1.bed /tmp/tmpx6i1e7r2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp43204s49/f1.bed /tmp/tmp43204s49/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp52x0vg1c/f1.bed /tmp/tmp52x0vg1c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgxkj9826/f1.bed /tmp/tmpgxkj9826/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_5xrrcst/f1.bed /tmp/tmp_5xrrcst/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpddpnfl_2/f1.bed /tmp/tmpddpnfl_2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3pfpob_0/f1.bed /tmp/tmp3pfpob_0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyia37je2/f1.bed /tmp/tmpyia37je2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsu7d3n6_/f1.bed /tmp/tmpsu7d3n6_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxlacok3p/f1.bed /tmp/tmpxlacok3p/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvp84c08d/f1.bed /tmp/tmpvp84c08d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphd793_g8/f1.bed /tmp/tmphd793_g8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnl_hu7op/f1.bed /tmp/tmpnl_hu7op/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_er874ug/f1.bed /tmp/tmp_er874ug/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp25q5lw3u/f1.bed /tmp/tmp25q5lw3u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_9bctqfl/f1.bed /tmp/tmp_9bctqfl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp4l7ecez/f1.bed /tmp/tmpp4l7ecez/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp988uglve/f1.bed /tmp/tmp988uglve/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8cxnrkio/f1.bed /tmp/tmp8cxnrkio/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpia5i4o8y/f1.bed /tmp/tmpia5i4o8y/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvnnt_iol/f1.bed /tmp/tmpvnnt_iol/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8r2pkei4/f1.bed /tmp/tmp8r2pkei4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfeqctu22/f1.bed /tmp/tmpfeqctu22/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp96reum_z/f1.bed /tmp/tmp96reum_z/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn2ei43vb/f1.bed /tmp/tmpn2ei43vb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3wdqfrcg/f1.bed /tmp/tmp3wdqfrcg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkdzcpvc0/f1.bed /tmp/tmpkdzcpvc0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbkojst2h/f1.bed /tmp/tmpbkojst2h/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp709nn381/f1.bed /tmp/tmp709nn381/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg3t90bxc/f1.bed /tmp/tmpg3t90bxc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6q3wfe3c/f1.bed /tmp/tmp6q3wfe3c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj7syeiip/f1.bed /tmp/tmpj7syeiip/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp84qnvzr7/f1.bed /tmp/tmp84qnvzr7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsjx8rrv5/f1.bed /tmp/tmpsjx8rrv5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpho47a4kh/f1.bed /tmp/tmpho47a4kh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdzofjluj/f1.bed /tmp/tmpdzofjluj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5u1qy3hg/f1.bed /tmp/tmp5u1qy3hg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptf2alz67/f1.bed /tmp/tmptf2alz67/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy9rsgis6/f1.bed /tmp/tmpy9rsgis6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzbjreoeo/f1.bed /tmp/tmpzbjreoeo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpapq55dgc/f1.bed /tmp/tmpapq55dgc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe34g8551/f1.bed /tmp/tmpe34g8551/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyocw4ymi/f1.bed /tmp/tmpyocw4ymi/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi5qr66uq/f1.bed /tmp/tmpi5qr66uq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm4lruuhw/f1.bed /tmp/tmpm4lruuhw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7ax_c3_a/f1.bed /tmp/tmp7ax_c3_a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl_mu4gaz/f1.bed /tmp/tmpl_mu4gaz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbcrnh44i/f1.bed /tmp/tmpbcrnh44i/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9g2u5si2/f1.bed /tmp/tmp9g2u5si2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_fywlmxj/f1.bed /tmp/tmp_fywlmxj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpipco_w1x/f1.bed /tmp/tmpipco_w1x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6gd2vkjk/f1.bed /tmp/tmp6gd2vkjk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn30algc6/f1.bed /tmp/tmpn30algc6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7u61_jy3/f1.bed /tmp/tmp7u61_jy3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8rfz2pzj/f1.bed /tmp/tmp8rfz2pzj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyo2lo1i2/f1.bed /tmp/tmpyo2lo1i2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk3gn0s12/f1.bed /tmp/tmpk3gn0s12/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp91hlbh66/f1.bed /tmp/tmp91hlbh66/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprzbsz5o3/f1.bed /tmp/tmprzbsz5o3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp70vhbf_r/f1.bed /tmp/tmp70vhbf_r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo6hvkgoz/f1.bed /tmp/tmpo6hvkgoz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu3cg5m3z/f1.bed /tmp/tmpu3cg5m3z/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcsiyk0qn/f1.bed /tmp/tmpcsiyk0qn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_jaccard[False] ______________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:363: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:378: in test_jaccard result = gr.stats.jaccard(gr2, strandedness=strandedness) pyranges/statistics.py:766: in jaccard for v in self.set_intersect(other).lengths(as_dict=True).values()) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_jaccard( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain4-method_chain4] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 172 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ___________ test_three_in_a_row[strandedness_chain38-method_chain38] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_set_union[same] _____________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:149: in test_set_union result = gr.set_union(gr2, strandedness=strandedness) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_union( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmpalzozfk6/f1.bed /tmp/tmpalzozfk6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7af1od31/f1.bed /tmp/tmp7af1od31/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu0hnzwe9/f1.bed /tmp/tmpu0hnzwe9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdm_kxf4x/f1.bed /tmp/tmpdm_kxf4x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw2iwz5o6/f1.bed /tmp/tmpw2iwz5o6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1itxdetw/f1.bed /tmp/tmp1itxdetw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc1t78g4d/f1.bed /tmp/tmpc1t78g4d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptddw65_p/f1.bed /tmp/tmptddw65_p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1usi5svf/f1.bed /tmp/tmp1usi5svf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8bhk833s/f1.bed /tmp/tmp8bhk833s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmrew7gam/f1.bed /tmp/tmpmrew7gam/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppkgp2t31/f1.bed /tmp/tmppkgp2t31/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4zau4l7q/f1.bed /tmp/tmp4zau4l7q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmz08vlg6/f1.bed /tmp/tmpmz08vlg6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpky8fc9ye/f1.bed /tmp/tmpky8fc9ye/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpevzwsbe1/f1.bed /tmp/tmpevzwsbe1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxm5nc65i/f1.bed /tmp/tmpxm5nc65i/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppj1rn98a/f1.bed /tmp/tmppj1rn98a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmmltyuwx/f1.bed /tmp/tmpmmltyuwx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6jj79irz/f1.bed /tmp/tmp6jj79irz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu3c84olx/f1.bed /tmp/tmpu3c84olx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpklluqr92/f1.bed /tmp/tmpklluqr92/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphk1rn7w2/f1.bed /tmp/tmphk1rn7w2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwb0_g5wq/f1.bed /tmp/tmpwb0_g5wq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0d1qh79a/f1.bed /tmp/tmp0d1qh79a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4pffdl_5/f1.bed /tmp/tmp4pffdl_5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp15b815oz/f1.bed /tmp/tmp15b815oz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv19hlysl/f1.bed /tmp/tmpv19hlysl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2jqxoyb9/f1.bed /tmp/tmp2jqxoyb9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplb2uc9zu/f1.bed /tmp/tmplb2uc9zu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa54nn9b5/f1.bed /tmp/tmpa54nn9b5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxqgogb3r/f1.bed /tmp/tmpxqgogb3r/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj_4ai7by/f1.bed /tmp/tmpj_4ai7by/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp38dj8yx_/f1.bed /tmp/tmp38dj8yx_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkmus1sp7/f1.bed /tmp/tmpkmus1sp7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpci80ys2i/f1.bed /tmp/tmpci80ys2i/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpliqp089r/f1.bed /tmp/tmpliqp089r/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj95z74yu/f1.bed /tmp/tmpj95z74yu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1p8rlhf6/f1.bed /tmp/tmp1p8rlhf6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0rgbv8w9/f1.bed /tmp/tmp0rgbv8w9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0smvtcgd/f1.bed /tmp/tmp0smvtcgd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp72oc362k/f1.bed /tmp/tmp72oc362k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4heairtd/f1.bed /tmp/tmp4heairtd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6hxley5p/f1.bed /tmp/tmp6hxley5p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyfiwa3v9/f1.bed /tmp/tmpyfiwa3v9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvm8exuf1/f1.bed /tmp/tmpvm8exuf1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq63zupse/f1.bed /tmp/tmpq63zupse/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpizzvd7a2/f1.bed /tmp/tmpizzvd7a2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvw67d9lh/f1.bed /tmp/tmpvw67d9lh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpebyrwboa/f1.bed /tmp/tmpebyrwboa/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpevsdyori/f1.bed /tmp/tmpevsdyori/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpejg8p90w/f1.bed /tmp/tmpejg8p90w/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1lpqyxoc/f1.bed /tmp/tmp1lpqyxoc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq691l9ep/f1.bed /tmp/tmpq691l9ep/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpht0zzt4d/f1.bed /tmp/tmpht0zzt4d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjuu3638v/f1.bed /tmp/tmpjuu3638v/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdy07d38j/f1.bed /tmp/tmpdy07d38j/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfc68k77q/f1.bed /tmp/tmpfc68k77q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6qjjul8e/f1.bed /tmp/tmp6qjjul8e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxc6d452c/f1.bed /tmp/tmpxc6d452c/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxznkzqyk/f1.bed /tmp/tmpxznkzqyk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpirv61hew/f1.bed /tmp/tmpirv61hew/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1qlxlwfc/f1.bed /tmp/tmp1qlxlwfc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu4t9w38w/f1.bed /tmp/tmpu4t9w38w/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw0nh647v/f1.bed /tmp/tmpw0nh647v/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp88opvmw/f1.bed /tmp/tmpp88opvmw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphv6i6fqa/f1.bed /tmp/tmphv6i6fqa/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxxfi38bn/f1.bed /tmp/tmpxxfi38bn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp12uz4oqh/f1.bed /tmp/tmp12uz4oqh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnqhfizha/f1.bed /tmp/tmpnqhfizha/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps9tl8ac7/f1.bed /tmp/tmps9tl8ac7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnzhdzj15/f1.bed /tmp/tmpnzhdzj15/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6y22oh_k/f1.bed /tmp/tmp6y22oh_k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp62xaxjd/f1.bed /tmp/tmpp62xaxjd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphdeijyye/f1.bed /tmp/tmphdeijyye/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgr2ipuua/f1.bed /tmp/tmpgr2ipuua/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpthqm9nsi/f1.bed /tmp/tmpthqm9nsi/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzf7flzle/f1.bed /tmp/tmpzf7flzle/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxz8zucde/f1.bed /tmp/tmpxz8zucde/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkfjx_pke/f1.bed /tmp/tmpkfjx_pke/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmyq72h1e/f1.bed /tmp/tmpmyq72h1e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb8b4pnug/f1.bed /tmp/tmpb8b4pnug/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1kfir7oo/f1.bed /tmp/tmp1kfir7oo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3q7sfzrd/f1.bed /tmp/tmp3q7sfzrd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjywei_9o/f1.bed /tmp/tmpjywei_9o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphhqc3d7v/f1.bed /tmp/tmphhqc3d7v/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4tz2kyua/f1.bed /tmp/tmp4tz2kyua/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgovcpvux/f1.bed /tmp/tmpgovcpvux/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr09g5u94/f1.bed /tmp/tmpr09g5u94/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwy4csavp/f1.bed /tmp/tmpwy4csavp/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb8ff8w0z/f1.bed /tmp/tmpb8ff8w0z/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdex9yitl/f1.bed /tmp/tmpdex9yitl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8dmocujm/f1.bed /tmp/tmp8dmocujm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_i14sxvn/f1.bed /tmp/tmp_i14sxvn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf0b21h4e/f1.bed /tmp/tmpf0b21h4e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplj91w0jz/f1.bed /tmp/tmplj91w0jz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_pvmxy0f/f1.bed /tmp/tmp_pvmxy0f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt95dwkhj/f1.bed /tmp/tmpt95dwkhj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcbv0etg3/f1.bed /tmp/tmpcbv0etg3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6e_y9hae/f1.bed /tmp/tmp6e_y9hae/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyph72_xb/f1.bed /tmp/tmpyph72_xb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqkvrt1cf/f1.bed /tmp/tmpqkvrt1cf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvaizm841/f1.bed /tmp/tmpvaizm841/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpiolzuqnm/f1.bed /tmp/tmpiolzuqnm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1_p8_fjr/f1.bed /tmp/tmp1_p8_fjr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprtn5fer5/f1.bed /tmp/tmprtn5fer5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphaacp_9l/f1.bed /tmp/tmphaacp_9l/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppyfeihjj/f1.bed /tmp/tmppyfeihjj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprgt6_1ui/f1.bed /tmp/tmprgt6_1ui/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn1v4tqwq/f1.bed /tmp/tmpn1v4tqwq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzppervoy/f1.bed /tmp/tmpzppervoy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf29cycgs/f1.bed /tmp/tmpf29cycgs/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcrfta2ms/f1.bed /tmp/tmpcrfta2ms/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzipagcp6/f1.bed /tmp/tmpzipagcp6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1246_84b/f1.bed /tmp/tmp1246_84b/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpge_zr929/f1.bed /tmp/tmpge_zr929/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvitl10x5/f1.bed /tmp/tmpvitl10x5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3g14hb4i/f1.bed /tmp/tmp3g14hb4i/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpexc6z7rk/f1.bed /tmp/tmpexc6z7rk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9h7ux_08/f1.bed /tmp/tmp9h7ux_08/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj0fn6ol6/f1.bed /tmp/tmpj0fn6ol6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcfcluyqa/f1.bed /tmp/tmpcfcluyqa/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz4gj9zhq/f1.bed /tmp/tmpz4gj9zhq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpifqtzfi5/f1.bed /tmp/tmpifqtzfi5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4_30ukh_/f1.bed /tmp/tmp4_30ukh_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpncz_pp5f/f1.bed /tmp/tmpncz_pp5f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6lzpe0me/f1.bed /tmp/tmp6lzpe0me/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp451gbd23/f1.bed /tmp/tmp451gbd23/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6oacm56h/f1.bed /tmp/tmp6oacm56h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcvw709p8/f1.bed /tmp/tmpcvw709p8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdpatm9me/f1.bed /tmp/tmpdpatm9me/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph94mty6t/f1.bed /tmp/tmph94mty6t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbril1cul/f1.bed /tmp/tmpbril1cul/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk8hbvfd0/f1.bed /tmp/tmpk8hbvfd0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpncfz4ug1/f1.bed /tmp/tmpncfz4ug1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqdx04hdv/f1.bed /tmp/tmpqdx04hdv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdaj27sj8/f1.bed /tmp/tmpdaj27sj8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8ab7pa47/f1.bed /tmp/tmp8ab7pa47/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6rdnyiru/f1.bed /tmp/tmp6rdnyiru/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0aqdckh6/f1.bed /tmp/tmp0aqdckh6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzen5g907/f1.bed /tmp/tmpzen5g907/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq08u76av/f1.bed /tmp/tmpq08u76av/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2zxjevbr/f1.bed /tmp/tmp2zxjevbr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9fcit41x/f1.bed /tmp/tmp9fcit41x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0cshjgxd/f1.bed /tmp/tmp0cshjgxd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc6w2yox6/f1.bed /tmp/tmpc6w2yox6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt2fap5kw/f1.bed /tmp/tmpt2fap5kw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvb2zoyjr/f1.bed /tmp/tmpvb2zoyjr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyg11s4ud/f1.bed /tmp/tmpyg11s4ud/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw3cee3ju/f1.bed /tmp/tmpw3cee3ju/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpanfims_a/f1.bed /tmp/tmpanfims_a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyizzuejo/f1.bed /tmp/tmpyizzuejo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpch1m2jd1/f1.bed /tmp/tmpch1m2jd1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoc08apuf/f1.bed /tmp/tmpoc08apuf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvyxmktmw/f1.bed /tmp/tmpvyxmktmw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0l07et02/f1.bed /tmp/tmp0l07et02/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppbgmxtp7/f1.bed /tmp/tmppbgmxtp7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj9km8282/f1.bed /tmp/tmpj9km8282/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8hi2b3mx/f1.bed /tmp/tmp8hi2b3mx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9bc40gky/f1.bed /tmp/tmp9bc40gky/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1ysamo2o/f1.bed /tmp/tmp1ysamo2o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvuamza1p/f1.bed /tmp/tmpvuamza1p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph1no0o_7/f1.bed /tmp/tmph1no0o_7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprpio_ngr/f1.bed /tmp/tmprpio_ngr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp96styom8/f1.bed /tmp/tmp96styom8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8u6cc08s/f1.bed /tmp/tmp8u6cc08s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbf3pzjxn/f1.bed /tmp/tmpbf3pzjxn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps3z2x45h/f1.bed /tmp/tmps3z2x45h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2oq1sj4_/f1.bed /tmp/tmp2oq1sj4_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjrz36lmz/f1.bed /tmp/tmpjrz36lmz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0p4owz04/f1.bed /tmp/tmp0p4owz04/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm8kj5bgu/f1.bed /tmp/tmpm8kj5bgu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpojldmigk/f1.bed /tmp/tmpojldmigk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnlnu17v7/f1.bed /tmp/tmpnlnu17v7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp04o3yj31/f1.bed /tmp/tmp04o3yj31/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdb7pwlzi/f1.bed /tmp/tmpdb7pwlzi/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp4i6_mrr/f1.bed /tmp/tmpp4i6_mrr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvh1e2dlr/f1.bed /tmp/tmpvh1e2dlr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqdoxis2a/f1.bed /tmp/tmpqdoxis2a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgfm3z4kx/f1.bed /tmp/tmpgfm3z4kx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp31105dof/f1.bed /tmp/tmp31105dof/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxg_x7br_/f1.bed /tmp/tmpxg_x7br_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpncmbj1y8/f1.bed /tmp/tmpncmbj1y8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphxsk6qim/f1.bed /tmp/tmphxsk6qim/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuc78nrxc/f1.bed /tmp/tmpuc78nrxc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkce7ytiv/f1.bed /tmp/tmpkce7ytiv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp04_o0hid/f1.bed /tmp/tmp04_o0hid/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp55f82b3b/f1.bed /tmp/tmp55f82b3b/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpodixbieb/f1.bed /tmp/tmpodixbieb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpydv1jvo_/f1.bed /tmp/tmpydv1jvo_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpll4m7pgr/f1.bed /tmp/tmpll4m7pgr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5var7fjn/f1.bed /tmp/tmp5var7fjn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp59dnltw0/f1.bed /tmp/tmp59dnltw0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv3ornetb/f1.bed /tmp/tmpv3ornetb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj1t9n1tj/f1.bed /tmp/tmpj1t9n1tj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz5c48uh9/f1.bed /tmp/tmpz5c48uh9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpetzbu47e/f1.bed /tmp/tmpetzbu47e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpio4n_qjn/f1.bed /tmp/tmpio4n_qjn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprfyvc97j/f1.bed /tmp/tmprfyvc97j/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr6hye9zh/f1.bed /tmp/tmpr6hye9zh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvjccme_3/f1.bed /tmp/tmpvjccme_3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp94strsnv/f1.bed /tmp/tmp94strsnv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnjfe2ojh/f1.bed /tmp/tmpnjfe2ojh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________________ test_jaccard[same] ______________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:363: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:378: in test_jaccard result = gr.stats.jaccard(gr2, strandedness=strandedness) pyranges/statistics.py:766: in jaccard for v in self.set_intersect(other).lengths(as_dict=True).values()) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_jaccard( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain5-method_chain5] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ___________ test_three_in_a_row[strandedness_chain39-method_chain39] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain6-method_chain6] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 181 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ___________ test_three_in_a_row[strandedness_chain40-method_chain40] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain7-method_chain7] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 122 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ___________ test_three_in_a_row[strandedness_chain41-method_chain41] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2CAA0YUCgIAAEAAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain8-method_chain8] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain42-method_chain42] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'set_union'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3504026 | 3505054 | a | 0 | - | E | chr7 | 3504026 | 3505054 | a | 0 | - | E | chr7 | 3529015 | 3530043 | a | 0 | - | E | chr7 | 3504026 | 3505054 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 17665 | 20738 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 273 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAR0L/LWBgEGARoFAgEVAAUEAAECABwDAQAABgMBVTXZNgEBAHk1d5kAAwQDBQMBEwMAAQABFwIAHgIBAQEEAQAAAQAAAQAIAEUADwMADAAAAA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain9-method_chain9] ____________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain43-method_chain43] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 157 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain10-method_chain10] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain11-method_chain11] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain45-method_chain45] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2653487 | 2655024 | a | 0 | - | E | chr1 | 5034658 | 5036403 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2653487 | 2653489 | a | 0 | - | E | chr1 | 20017 | 21554 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 769 | 770 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY+Ga1vuXkSez7i0DNwMDAx8jIwMXg7ZGrR43Y7nPpYUMfAx+bAycjBJsFxgYgHIMLFxsvJiKQcoMeBn52RgY2BkYGRjZxBjcNRlALAZmBgZWoFpGAKoYDTg=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain12-method_chain12] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 105 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain47-method_chain47] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 196609 | 196610 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 518145 | 518146 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 154 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2CAAlYGRgYOIAYDZiBmAjEYlctYUyDy7C+gKgEcSQIM') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain13-method_chain13] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________ test_k_nearest[downstream-False-opposite-last] ________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 85027 | 86820 | a | 0 | + | | | chr1 | 85027 | 86820 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 259 | 271 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY8zsqHBjS5mq08HAzcjIAISMPkoMwuwM7EA2AyOEBBFAiomBlYGbgQEAsSQEIg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2SAAEYGBGDEFGMEAACRAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphb0mf4o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphb0mf4o0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7p0i4hny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7p0i4hny/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpul5yx8el/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpul5yx8el/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnqck1axt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnqck1axt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzhdtm2f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhdtm2f5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsjel6qrh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsjel6qrh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmtmxy7tx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmtmxy7tx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimkpmhwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimkpmhwj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp98xrw8ej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98xrw8ej/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe7v350af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7v350af/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnbw8q4zd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnbw8q4zd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd97s82co/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd97s82co/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8kmve5y9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8kmve5y9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2idka9p0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2idka9p0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi8yqeb7b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8yqeb7b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__vqh2gl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__vqh2gl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp109wjw3m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp109wjw3m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8_6fbs7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_6fbs7s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3vbzg4hi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vbzg4hi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa833vlr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa833vlr5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz6sbp0aa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz6sbp0aa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwq213dyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwq213dyy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptnt71lr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptnt71lr5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo2vq8rsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2vq8rsn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd8jm68a2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd8jm68a2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpffuiowam/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffuiowam/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxps2yfr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxps2yfr0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu0a47bgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0a47bgd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy0w1owlw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0w1owlw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmmh0tk7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmh0tk7q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfx30hp4t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfx30hp4t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsix35p0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsix35p0h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwx6wyq33/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwx6wyq33/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpryhyd4rm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpryhyd4rm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplagj6g6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplagj6g6k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp57tp6l8l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57tp6l8l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbec47oqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbec47oqa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6fo_isg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6fo_isg9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpksezjbwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksezjbwa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeln3pyx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeln3pyx9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnqsq_yzd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnqsq_yzd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwlmvwqj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlmvwqj4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm2pqws40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm2pqws40/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbtcw78kk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbtcw78kk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkatg5edc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkatg5edc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7mol38px/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mol38px/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd7uen5yx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7uen5yx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn8s63kfo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8s63kfo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9a_8i8h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9a_8i8h_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl0q3ntm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0q3ntm5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmr29gjc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmr29gjc8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp462set48/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp462set48/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv_iyjsa5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_iyjsa5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfxh_6jn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfxh_6jn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ugvgz_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ugvgz_x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfwba_1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfwba_1a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm1tylbea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1tylbea/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpucamjttr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpucamjttr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqlsds5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqlsds5a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplcmv_9bq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcmv_9bq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi4yl8cgq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4yl8cgq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe9sxnazu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9sxnazu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8sygthuv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8sygthuv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9n7ykjs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9n7ykjs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0_zzg16z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_zzg16z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppps56nje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppps56nje/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv4p5b56v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv4p5b56v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_mfn1qt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_mfn1qt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqbkt_dnk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbkt_dnk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppa84a6c0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppa84a6c0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpas0a0wvg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas0a0wvg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzzrjghlk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzrjghlk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_u5rt6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_u5rt6d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_z49x_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_z49x_h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl3ax1k2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl3ax1k2n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsfm1ethj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfm1ethj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfn9_6ti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfn9_6ti/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoiuqvhbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoiuqvhbc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxqfp_qqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqfp_qqg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph5ekz0iv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5ekz0iv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpksex_vly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksex_vly/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0yqsjuwl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0yqsjuwl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp32m95251/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32m95251/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5j5o3_id/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5j5o3_id/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw3bi1681/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3bi1681/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4gsw21dr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4gsw21dr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpckr2396c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpckr2396c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6i3qxm3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i3qxm3n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkh7fd8g1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkh7fd8g1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvk2qr7av/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvk2qr7av/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ezeewqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ezeewqh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbgpl8xtz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgpl8xtz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5e2lqc6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5e2lqc6v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpetj9u9rs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetj9u9rs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp20zk917o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20zk917o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw97k0blo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw97k0blo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfr7rqtr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfr7rqtr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpze9jmqv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpze9jmqv5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhw2e744/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhw2e744/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpck40d5vw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpck40d5vw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkvhwv4au/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvhwv4au/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyezmbnzp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyezmbnzp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg4np073f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4np073f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpan209nwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpan209nwa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2xilj6w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2xilj6w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmhtl_uet/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmhtl_uet/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwefhn34j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwefhn34j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjdm0c39p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjdm0c39p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymbb7juy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymbb7juy/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain14-method_chain14] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 219 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain49-method_chain49] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 226 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-False-same-last] __________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = 'downstream', overlap = False, strandedness = 'same' ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how='downstream', E overlap=False, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 E (and 41 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:55: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg5lgoeam/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5lgoeam/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9djp_6ur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9djp_6ur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5swt3u8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5swt3u8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxdo7kivv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdo7kivv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymjz9b9g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymjz9b9g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuds7xgr2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuds7xgr2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz5x__07y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5x__07y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1luxid6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1luxid6j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8yw08kgy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8yw08kgy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0_m7mjw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_m7mjw1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2youqx68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2youqx68/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6dgt5ukh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6dgt5ukh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9uw8yskg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9uw8yskg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz108t8pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz108t8pb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpknizbabn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpknizbabn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7w3uzuh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7w3uzuh5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp35ppi4sb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35ppi4sb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt85gejgw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt85gejgw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphz1ry690/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphz1ry690/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpru2sjw9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpru2sjw9v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7xgs34r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7xgs34r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzpvvue1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzpvvue1e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpipkjlbjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipkjlbjf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8uh5__52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8uh5__52/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3afd58b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3afd58b3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqsldwwm1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqsldwwm1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu_51qky7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_51qky7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkuxwtxig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkuxwtxig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpouif2rar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpouif2rar/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu13d_r_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu13d_r_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp33zrpn_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33zrpn_t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymo0k8cz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymo0k8cz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp842uzrzv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp842uzrzv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl3uk_7p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl3uk_7p4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpek690axd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpek690axd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbaahn8fr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbaahn8fr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt7vwbwpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7vwbwpl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzzww5mcd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzww5mcd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqu24gq7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqu24gq7z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpijw4701b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijw4701b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphhw6po0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphhw6po0m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf84p4cp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf84p4cp9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk9ufj1m8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9ufj1m8/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. _________________ test_k_nearest[downstream-False-False-last] __________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = 'downstream', overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how='downstream', E overlap=False, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:46 E (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:55: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa4b15u2j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4b15u2j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1px_1okl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1px_1okl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuj_oexl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuj_oexl9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7i1dhff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7i1dhff/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzugxgmfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzugxgmfa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp9igtsg7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp9igtsg7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdjivuuqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdjivuuqp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbf3kvunc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbf3kvunc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp81jlzsil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81jlzsil/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5gbjq9qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gbjq9qx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr4_4adc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr4_4adc5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy65pm4y7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy65pm4y7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy6z69mru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6z69mru/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuhki2qp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuhki2qp3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo5oegqpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo5oegqpi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimmgdgcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimmgdgcg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2zas0xgl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zas0xgl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5qw5v_8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qw5v_8s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa1ksoqpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1ksoqpk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvcisdxm9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcisdxm9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw3rj6yoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3rj6yoy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1zi52mc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1zi52mc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9i9suk9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9i9suk9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoz9_tn9x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz9_tn9x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphpq5m9nc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphpq5m9nc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpop5xl53i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpop5xl53i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu1_uxp25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu1_uxp25/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7bfqhxkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bfqhxkw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptgndwqjw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptgndwqjw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4q4olhk8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4q4olhk8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaded5f34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaded5f34/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphgag9g07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgag9g07/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_o05x8t6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_o05x8t6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm5iio0sw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5iio0sw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppvphv9r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvphv9r6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbujv0lbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbujv0lbn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgtavoi0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgtavoi0d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2eq988u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2eq988u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpau48woy0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpau48woy0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjh6_rnoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh6_rnoh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsi1w1kyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsi1w1kyn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxaa9sj64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxaa9sj64/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpch5o2xpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpch5o2xpk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4bwe0m1b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bwe0m1b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuijxy2ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuijxy2ua/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0oeje1tx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0oeje1tx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzeqxw8zg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzeqxw8zg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplvkfus4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvkfus4a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw7uz4sxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7uz4sxo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4umm36hc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4umm36hc/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain15-method_chain15] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5 | 7 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 514 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkAAJ2BkYgZGAEYRCDhYEBzGcQZIAKMUJEGAAENwAr') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain50-method_chain50] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________ test_k_nearest[downstream-True-opposite-last] _________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = 'downstream', overlap = True, strandedness = 'opposite' ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how='downstream', E overlap=True, E strandedness='opposite', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 132356 | 134149 | a | 0 | + | E | chr1 | 132356 | 135944 | a | 0 | + | E | chr1 | 132356 | 138503 | a | 0 | + | E | chr1 | 132356 | 138506 | a | 0 | + | E | chr1 | 132356 | 132876 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5695 | 8527 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 E (and 41 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY+T0ri9jlCoqX8LomsyyjTFVUKeWsZoBCsSZWJkZGRjZGRgZDfmYGZl4JZgYmRklWBlZYpnYgfJgPQxAFQwMnAxidowMytz8QFEABGsJGA==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:55: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp002l3512/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp002l3512/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx73z1mtk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx73z1mtk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5fv3dxa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5fv3dxa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpej5ico_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpej5ico_p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwh1562c_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwh1562c_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq24ohwo3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq24ohwo3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprof6rm0g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprof6rm0g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9a5x5fkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9a5x5fkx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ly9e_je/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ly9e_je/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9d9f16r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9d9f16r6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2xr6o9mv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2xr6o9mv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu5xcnp3s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5xcnp3s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfw9xdoc4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfw9xdoc4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqepjhp9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqepjhp9r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplzhoayz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzhoayz7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5w1e0lx3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5w1e0lx3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj9p1szl4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9p1szl4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkmfgms58/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmfgms58/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbi8sh1eo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbi8sh1eo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9wj1wjt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9wj1wjt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf8b7ztm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8b7ztm7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2_bj81x_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2_bj81x_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9nj9xjtq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9nj9xjtq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpedkr6z5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedkr6z5l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp81ysbg5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81ysbg5g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1j_97xmu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1j_97xmu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ifmj00w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ifmj00w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0sc57ldy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0sc57ldy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3erch2yj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3erch2yj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6iy9s6he/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6iy9s6he/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwc2ji05y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwc2ji05y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpks615i_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpks615i_h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq4zas0ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq4zas0ox/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpui6reh0l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpui6reh0l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphdj4icm4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphdj4icm4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3gll914j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3gll914j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0l_1hrkb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0l_1hrkb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr2khd4p9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr2khd4p9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_c_xa_vp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_c_xa_vp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwr34khcu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwr34khcu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0acomysh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0acomysh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprkd3rlna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkd3rlna/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpansliien/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpansliien/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz8m0icds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8m0icds/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5avqh299/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5avqh299/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgm1_nops/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgm1_nops/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ht0r3h5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ht0r3h5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp81fwim0z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81fwim0z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf89lczbk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf89lczbk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2lv0ferr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lv0ferr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf03ovgv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf03ovgv_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp86s7lekf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86s7lekf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp95g885mk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95g885mk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpucvvsqxn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpucvvsqxn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8or1za1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8or1za1f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp73xp9k0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp73xp9k0_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplmolg8ey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmolg8ey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4b6imz0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4b6imz0m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphiue21q8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphiue21q8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt0lruwdk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0lruwdk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxs0ljou3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxs0ljou3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9q3dpgbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9q3dpgbx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy_tttacn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_tttacn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprhj2cmyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhj2cmyo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyz3pof53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyz3pof53/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmploddevc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmploddevc7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfhnj216u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfhnj216u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprlhkbvqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprlhkbvqp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp81h3izbh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81h3izbh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmg4mev9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmg4mev9i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfaqclspe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfaqclspe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__8tbtta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__8tbtta/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd61_2akc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd61_2akc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptcbl73t1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptcbl73t1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1m5vf83j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1m5vf83j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe70zgp44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe70zgp44/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuoqxypxy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuoqxypxy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprgaj3vnw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgaj3vnw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl6mbhyhp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6mbhyhp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4jbfk4_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jbfk4_w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7h06y3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7h06y3j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph6l3p5g7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6l3p5g7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpacrgcpxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpacrgcpxz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5p85kkrx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5p85kkrx/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain51-method_chain51] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain17-method_chain17] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8230453 | 8233268 | a | 0 | + | E | chr1 | 7913827 | 7923339 | a | 0 | - | E | chr1 | 8749740 | 8752555 | a | 0 | - | E | chr1 | 8230453 | 8233268 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr11 | 8230453 | 8233268 | a | 0 | - | E | chr12 | 146947 | 149762 | a | 0 | - | E | chr19 | 8230453 | 8233268 | a | 0 | - | E | chr19 | 4954810 | 4957625 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 853557 | 854582 | a | 0 | + | E | chr1 | 132354 | 133379 | a | 0 | + | E | chr1 | 853557 | 860485 | a | 0 | + | E | chr1 | 853557 | 854582 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr11 | 853557 | 854582 | a | 0 | + | E | chr12 | 853557 | 859200 | a | 0 | + | E | chr19 | 853557 | 854582 | a | 0 | + | E | chr19 | 2049 | 3074 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 769 | 1030 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 43 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY0s/EFvUsyaCudze2okxda+bdYCwEJPTHpUNr5+k/I7bFHWmiy342/fF2noL2NnZWVy8W7KYQvZnTWp8EsQktP2ycevZ+YwxUx2WsLOzlu44nHjhkFbZZBkGG34OBiFGFgYhTn4WbQZGVk5GTWYGbnk+ZnE+blZGI34GNU47fkZGey1uVnludgYubl4mRik2RgZpHn4Gl4qDScYczt6zdqowZrc2rbZm5mOyY2JlZAiunWaix2CrbaKqbq/LKa9lo/qYIYzrnzwrgzQ/AyMDIxvQ4UwsQIezAB3OBHI40GEsIFezgFzNYg90NQvI1cxEu5oR6Gp+PmZGuKv5gK7m58LtagYOBqhrhXnZwK5lUVXn5+Xk5+JhZWYQ4+Ljh7iWhYET6GQQkmQEkUDAxMDMwMMAkuIBigAAWvJO6g==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5445655 | 5451204 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5445655 | 5451204 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-True-same-last] ___________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = 'downstream', overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how='downstream', E overlap=True, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:55: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4xbpgnp1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xbpgnp1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbp9j1ml_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbp9j1ml_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi7vbhm68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7vbhm68/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptua7ehmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptua7ehmg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpts17livy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpts17livy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6xnap81o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xnap81o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpthrqtrgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpthrqtrgi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgeg3vt58/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgeg3vt58/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwnnj20ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwnnj20ig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ypqrkfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ypqrkfn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_kubam4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_kubam4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4yh9nmba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yh9nmba/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps_iob4qr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_iob4qr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpatudqwcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatudqwcg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02wn2zka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02wn2zka/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplbuc3jpd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbuc3jpd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbsbalc_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbsbalc_z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuxty4u8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuxty4u8s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ul201m5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ul201m5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf9nqplkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9nqplkk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpigxn5i7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigxn5i7q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc0ryxk6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0ryxk6k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_ts90gw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_ts90gw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprnefmu_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprnefmu_v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1s_fecxp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1s_fecxp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnm0chkc2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnm0chkc2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpie6st8v2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpie6st8v2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5gtq0q7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gtq0q7x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfk5lsuxs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfk5lsuxs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkfyat3go/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkfyat3go/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpadqkuy4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadqkuy4c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbf73r16x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbf73r16x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqs1fygfy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqs1fygfy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8r42e7in/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8r42e7in/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpchtl1sdd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchtl1sdd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjj1p8fvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjj1p8fvq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6of03lc9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6of03lc9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzlk7z10j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzlk7z10j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps9hdg6t8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9hdg6t8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcv80c8u4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcv80c8u4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprw_i52ui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprw_i52ui/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq34pyhpc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq34pyhpc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuwa0t9c1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwa0t9c1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy7v5xzmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7v5xzmz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0208duqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0208duqr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ify2zkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ify2zkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_1qjlku7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1qjlku7/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain52-method_chain52] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain19-method_chain19] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2503025 | 2505330 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 5 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2Bk4GAQUlVnYGQ0DK/5wAACQWqGBYwMXJxAJiOjpSoHI5BmYAIRvECKEQCGYgQI') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-True-False-last] __________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65793 | 70658 | a | 0 | - | | | chr21 | 1281 | 2350 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 939777 | 939791 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicHYqxDYAwEMR8/0RCip4GxqBnEkTHHKmYiq0os0ASKsuWVe6j+vk+HwJJDhszToIs9dqHaU+EWMEkY4yE/bDlGk5AA5SzBxw=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjl0q97py/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjl0q97py/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2apyq77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2apyq77/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphajwega7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphajwega7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkivwygus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkivwygus/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7pf6vjea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pf6vjea/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5rk60uaq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5rk60uaq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkc72au76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkc72au76/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmputf07xct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputf07xct/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6kd_c5yt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kd_c5yt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy66l1zkz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy66l1zkz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsl42y7ca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsl42y7ca/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjh7bdr6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh7bdr6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprsn_h3wq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprsn_h3wq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3j9erd0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3j9erd0p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuqh_iuud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqh_iuud/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgaw7c_3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgaw7c_3_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsjw4_x0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsjw4_x0v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpww2f2fu_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpww2f2fu_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphb4gxi77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphb4gxi77/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbciyw8zm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbciyw8zm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi6bx91ow/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi6bx91ow/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9ewb96p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9ewb96p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclv85378/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclv85378/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyi8p90rq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyi8p90rq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb93eg3bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb93eg3bo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgx2kdkvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgx2kdkvx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7ipqp4w1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ipqp4w1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimzojcli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimzojcli/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpde0ify9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpde0ify9v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph9u57ywt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9u57ywt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7486uj4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7486uj4c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp46qd94km/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46qd94km/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfhqapsc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfhqapsc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf9btlmlr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9btlmlr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkdjj297z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdjj297z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq3ww9kwe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3ww9kwe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2cq36njb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2cq36njb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp73qmt10e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp73qmt10e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl6_0o19l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6_0o19l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnfhto71x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfhto71x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpixoi7vie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixoi7vie/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp93wq6kqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93wq6kqa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_wb8l_fb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_wb8l_fb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplqkq9f3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqkq9f3t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa82j55rv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa82j55rv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4kbodj15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4kbodj15/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv3g2gr0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3g2gr0h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxs0k0fwc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxs0k0fwc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgn936db2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgn936db2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2uzw6ol2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uzw6ol2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4y96jxdj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4y96jxdj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp39uy3s5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39uy3s5a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdeuqsi0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdeuqsi0s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqbpic8hd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbpic8hd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzq_2_osr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzq_2_osr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjvbsw293/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvbsw293/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppkm9gpet/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppkm9gpet/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptex7uixn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptex7uixn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp34nd6ghx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34nd6ghx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbkgswqo9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkgswqo9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpssbp94i7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssbp94i7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqgbs6v9e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqgbs6v9e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp97cbnopk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97cbnopk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppwalk73z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwalk73z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp08mpv_c1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08mpv_c1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1q8l9b0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q8l9b0d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4f1c685s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f1c685s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzw5jehu6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzw5jehu6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbmmgfqlo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmmgfqlo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo3ltn7fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo3ltn7fa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpphm6mdi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpphm6mdi6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq_az2ywg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_az2ywg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp28yvvlys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28yvvlys/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgy287eih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy287eih/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzlhqhc7h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzlhqhc7h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp45jmf8ca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45jmf8ca/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjlllxzkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjlllxzkd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1sck4m7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sck4m7c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm_t8dj_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_t8dj_z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmy_92tn2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmy_92tn2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd1m9w6v_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd1m9w6v_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppucajtvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppucajtvl/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_coverage[False] _____________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5_afka1m/f1.bed -b /tmp/tmp5_afka1m/f2.bed Chromosome Start End Name Score Strand 0 chr1 3231906 3239642 a 0 + 1 chr1 2627893 2636373 a 0 + 2 chr1 474077 480374 a 0 - 3 chr1 2627893 2630197 a 0 - 4 chr2 4630050 4630051 a 0 + 5 chr7 7312476 7316009 a 0 + 6 chr8 2627893 2636904 a 0 - 7 chr10 2627893 2636650 a 0 + 8 chr11 7513730 7517678 a 0 + 9 chr18 8846109 8850480 a 0 + 10 chr18 6445527 6455527 a 0 - Chromosome Start End Name Score Strand 0 chr1 9707255 9711450 a 0 + 1 chr5 4205899 4208258 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp38nxa4ks/f1.bed -b /tmp/tmp38nxa4ks/f2.bed Chromosome Start End Name Score Strand 0 chr1 3231906 3239642 a 0 + 1 chr1 2627893 2636373 a 0 + 2 chr1 474077 480374 a 0 - 3 chr1 2627893 2630197 a 0 - 4 chr2 4630050 4630051 a 0 + 5 chr7 7312476 7316009 a 0 + 6 chr8 2627893 2636904 a 0 - 7 chr10 2627893 2636650 a 0 + 8 chr11 7513730 7517678 a 0 + 9 chr18 8846109 8850480 a 0 + 10 chr18 6445527 6455527 a 0 - Chromosome Start End Name Score Strand 0 chr1 3231906 3239642 a 0 + 1 chr1 2627893 2636373 a 0 + 2 chr1 474077 480374 a 0 - 3 chr1 2627893 2630197 a 0 - 4 chr2 4630050 4630051 a 0 + 5 chr7 7312476 7316009 a 0 + 6 chr8 2627893 2636904 a 0 - 7 chr10 2627893 2636650 a 0 + 8 chr11 7513730 7517678 a 0 + 9 chr18 8846109 8850480 a 0 + 10 chr18 6445527 6455527 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpq9rajd_g/f1.bed -b /tmp/tmpq9rajd_g/f2.bed Chromosome Start End Name Score Strand 0 chr1 5387 5398 a 0 - 1 chr1 5387 5398 a 0 - 2 chr1 5387 5398 a 0 - 3 chr13 336917 336928 a 0 + 4 chrX 5387 5398 a 0 + 5 chrY 590082 590093 a 0 - Chromosome Start End Name Score Strand 0 chr1 5588647 5593018 a 0 - 1 chr1 5005914 5005915 a 0 - 2 chr1 3922970 3925310 a 0 - 3 chr4 7312476 7314028 a 0 + 4 chr8 3231906 3234065 a 0 + 5 chr16 199066 202150 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpoepi5x24/f1.bed -b /tmp/tmpoepi5x24/f2.bed Chromosome Start End Name Score Strand 0 chr1 275462 275719 a 0 + 1 chr1 275462 280849 a 0 + 2 chr1 275462 280849 a 0 + 3 chr1 275462 280849 a 0 + 4 chr13 275462 276999 a 0 + 5 chrY 275462 280849 a 0 + Chromosome Start End Name Score Strand 0 chr1 262417 270360 a 0 + 1 chr1 394245 402188 a 0 - 2 chr1 65538 67080 a 0 - 3 chr4 3408940 3409709 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppqng_tub/f1.bed -b /tmp/tmppqng_tub/f2.bed Chromosome Start End Name Score Strand 0 chr1 275462 275719 a 0 + 1 chr1 275462 280849 a 0 + 2 chr1 275462 280849 a 0 + 3 chr1 275462 280849 a 0 + 4 chr13 275462 276999 a 0 + 5 chrY 275462 280849 a 0 + Chromosome Start End Name Score Strand 0 chr1 262417 270360 a 0 + 1 chr1 394245 402188 a 0 - 2 chr1 65538 67080 a 0 - 3 chr4 3408940 3409709 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0w0eho1_/f1.bed -b /tmp/tmp0w0eho1_/f2.bed Chromosome Start End Name Score Strand 0 chr1 275462 275719 a 0 + 1 chr1 275462 280849 a 0 + 2 chr1 275462 280849 a 0 + 3 chr1 275462 280849 a 0 + 4 chr13 275462 276999 a 0 + 5 chrY 275462 280849 a 0 + Chromosome Start End Name Score Strand 0 chr5 66822 67370 a 0 - 1 chr22 3801089 3801637 a 0 + 2 chr22 131073 131621 a 0 + 3 chr22 78088 78636 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2pvkz0r1/f1.bed -b /tmp/tmp2pvkz0r1/f2.bed Chromosome Start End Name Score Strand 0 chr1 275462 275719 a 0 + 1 chr1 275462 280849 a 0 + 2 chr1 275462 280849 a 0 + 3 chr1 275462 280849 a 0 + 4 chr13 275462 276999 a 0 + 5 chrY 275462 280849 a 0 + Chromosome Start End Name Score Strand 0 chr5 66822 66823 a 0 - 1 chr22 78088 78100 a 0 - 2 chr22 3801089 3801350 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpueqmb6sa/f1.bed -b /tmp/tmpueqmb6sa/f2.bed Chromosome Start End Name Score Strand 0 chr1 8058813 8058933 a 0 + 1 chr1 8058813 8065718 a 0 + 2 chr1 8058813 8061433 a 0 - 3 chr11 8058813 8068761 a 0 + 4 chr15 8058813 8060812 a 0 + 5 chr16 8058813 8063087 a 0 + 6 chr18 8058813 8058856 a 0 + 7 chr19 8058813 8063212 a 0 + 8 chr19 8058813 8064451 a 0 + 9 chrY 8058813 8065121 a 0 + 10 chrY 8058813 8063842 a 0 + Chromosome Start End Name Score Strand 0 chr12 6297678 6302134 a 0 + 1 chr12 9229645 9236528 a 0 + 2 chr12 4219962 4220977 a 0 + 3 chr12 204560 209811 a 0 + 4 chr12 1854539 1856591 a 0 - 5 chr12 377830 378052 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpe0b5mpp1/f1.bed -b /tmp/tmpe0b5mpp1/f2.bed Chromosome Start End Name Score Strand 0 chr1 5295711 5295729 a 0 + 1 chr1 1488883 1494011 a 0 - 2 chr1 6477646 6484314 a 0 - 3 chr1 655392 664112 a 0 - 4 chr6 655392 662060 a 0 - 5 chr12 655392 662060 a 0 - 6 chr21 655392 662060 a 0 + Chromosome Start End Name Score Strand 0 chr1 284 7529 a 0 + 1 chr1 3014668 3021913 a 0 + 2 chr1 4194424 4201669 a 0 + 3 chr1 589887 591363 a 0 - 4 chr1 3014668 3021913 a 0 - 5 chr1 787811 794033 a 0 - 6 chr1 3474998 3480451 a 0 - 7 chr7 7064874 7072826 a 0 + 8 chr9 138069 145314 a 0 + 9 chrX 2956702 2963947 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp00qilgwo/f1.bed -b /tmp/tmp00qilgwo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpldmrk750/f1.bed -b /tmp/tmpldmrk750/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa8hm8v4x/f1.bed -b /tmp/tmpa8hm8v4x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpcp1lyn1s/f1.bed -b /tmp/tmpcp1lyn1s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpmxht8kkt/f1.bed -b /tmp/tmpmxht8kkt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpivqj_xjo/f1.bed -b /tmp/tmpivqj_xjo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqq8_miku/f1.bed -b /tmp/tmpqq8_miku/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpij_mo9_l/f1.bed -b /tmp/tmpij_mo9_l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpys02h6gw/f1.bed -b /tmp/tmpys02h6gw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpn38nmxh_/f1.bed -b /tmp/tmpn38nmxh_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9ejjood2/f1.bed -b /tmp/tmp9ejjood2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyoxynzgb/f1.bed -b /tmp/tmpyoxynzgb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6uh19iyb/f1.bed -b /tmp/tmp6uh19iyb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpr3z3scri/f1.bed -b /tmp/tmpr3z3scri/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpmbvlnf13/f1.bed -b /tmp/tmpmbvlnf13/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppogrqfu2/f1.bed -b /tmp/tmppogrqfu2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpm0j59vgr/f1.bed -b /tmp/tmpm0j59vgr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1e107aj2/f1.bed -b /tmp/tmp1e107aj2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplaxpl5ic/f1.bed -b /tmp/tmplaxpl5ic/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp18nunxe6/f1.bed -b /tmp/tmp18nunxe6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpynm3xo24/f1.bed -b /tmp/tmpynm3xo24/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphwc6az0u/f1.bed -b /tmp/tmphwc6az0u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyy2u0v8j/f1.bed -b /tmp/tmpyy2u0v8j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphqruwfij/f1.bed -b /tmp/tmphqruwfij/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4xqh_v3u/f1.bed -b /tmp/tmp4xqh_v3u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgy7k13b5/f1.bed -b /tmp/tmpgy7k13b5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpoe271vew/f1.bed -b /tmp/tmpoe271vew/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3s82ol4b/f1.bed -b /tmp/tmp3s82ol4b/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr13 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3733421 3741042 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgf5g2o2v/f1.bed -b /tmp/tmpgf5g2o2v/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr13 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpax_cyuya/f1.bed -b /tmp/tmpax_cyuya/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 4132 a 0 + 1 chr1 1 4132 a 0 + Chromosome Start End Name Score Strand 0 chr1 8363817 8369312 a 0 + 1 chr1 8507630 8508636 a 0 + 2 chr1 4364752 4365027 a 0 - 3 chr1 3382503 3387577 a 0 - 4 chr4 8024920 8027109 a 0 + 5 chr5 8507630 8509819 a 0 + 6 chr10 8507630 8512598 a 0 + 7 chr16 8507630 8508390 a 0 + 8 chr19 8507630 8517520 a 0 + 9 chr20 7206881 7215366 a 0 + 10 chrX 910940 919028 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpchh307kr/f1.bed -b /tmp/tmpchh307kr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 4132 a 0 + 1 chr1 1 4132 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpane36hb2/f1.bed -b /tmp/tmpane36hb2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5750376 5751473 a 0 + 1 chr1 5750376 5758068 a 0 + 2 chr1 1016174 1021909 a 0 + 3 chr1 5750376 5757050 a 0 + 4 chr1 6168988 6176728 a 0 - 5 chr5 5750376 5756396 a 0 - 6 chr8 5750376 5758089 a 0 - 7 chr21 438865 444759 a 0 + 8 chrM 631232 632469 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyi0wr20c/f1.bed -b /tmp/tmpyi0wr20c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2913t8go/f1.bed -b /tmp/tmp2913t8go/f2.bed Chromosome Start End Name Score Strand 0 chr1 1847064 1857063 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 4976 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5mkf2cff/f1.bed -b /tmp/tmp5mkf2cff/f2.bed Chromosome Start End Name Score Strand 0 chr1 1847064 1857063 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpreku2_ok/f1.bed -b /tmp/tmpreku2_ok/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8795839 8803046 a 0 + 1 chr1 7532 17123 a 0 + 2 chr1 8819226 8825253 a 0 + 3 chr1 6115791 6121896 a 0 + 4 chr1 2835731 2844850 a 0 - 5 chr1 796975 796976 a 0 - 6 chr1 7838820 7848546 a 0 - 7 chr13 2880905 2885906 a 0 - 8 chr18 8819226 8827559 a 0 - 9 chr19 4497001 4504208 a 0 - 10 chrM 7623377 7631029 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgiq9lub_/f1.bed -b /tmp/tmpgiq9lub_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplvmgr8bj/f1.bed -b /tmp/tmplvmgr8bj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5650644 5656839 a 0 + 1 chr1 7622986 7625272 a 0 + 2 chr1 7622986 7626815 a 0 + 3 chr1 623714 627453 a 0 + 4 chr1 7622986 7627123 a 0 + 5 chr1 5629672 5633987 a 0 - 6 chr1 3983551 3991145 a 0 - 7 chr1 4094061 4099444 a 0 - 8 chr1 4072376 4079391 a 0 - 9 chr1 4863322 4867731 a 0 - 10 chr16 6094678 6098507 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpiees8wgb/f1.bed -b /tmp/tmpiees8wgb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp18u_rzrw/f1.bed -b /tmp/tmp18u_rzrw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr16 6273934 6275739 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp15h5fotd/f1.bed -b /tmp/tmp15h5fotd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_drl3sp3/f1.bed -b /tmp/tmp_drl3sp3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6712 a 0 + 1 chr1 1 6712 a 0 + Chromosome Start End Name Score Strand 0 chr1 8550004 8555812 a 0 - 1 chr10 3089674 3097299 a 0 - 2 chr10 3664196 3664784 a 0 - 3 chr17 9141514 9145509 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptqqthcgc/f1.bed -b /tmp/tmptqqthcgc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6712 a 0 + 1 chr1 1 6712 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp972cx5ah/f1.bed -b /tmp/tmp972cx5ah/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6832216 6836320 a 0 - 1 chr2 2248157 2250205 a 0 + 2 chr14 7079076 7079152 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxcwehcfs/f1.bed -b /tmp/tmpxcwehcfs/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpud59bs6s/f1.bed -b /tmp/tmpud59bs6s/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 246692 248688 a 0 + 1 chr1 4131715 4137547 a 0 - 2 chr1 5664215 5671504 a 0 - 3 chr5 5132228 5133719 a 0 - 4 chr6 3289532 3299295 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpst_zqggq/f1.bed -b /tmp/tmpst_zqggq/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprmukabw0/f1.bed -b /tmp/tmprmukabw0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7732624 7737206 a 0 + 1 chr1 5759392 5759641 a 0 + 2 chr1 5697581 5705533 a 0 + 3 chr1 9322916 9329418 a 0 - 4 chr1 5742897 5750644 a 0 - 5 chr1 3657109 3666795 a 0 - 6 chr5 6703307 6713306 a 0 + 7 chr12 9033490 9039417 a 0 - 8 chr21 9523570 9533256 a 0 - 9 chr22 6583282 6584298 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp07clc28_/f1.bed -b /tmp/tmp07clc28_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppijpucqf/f1.bed -b /tmp/tmppijpucqf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10001634 a 0 + 1 chr1 9890205 9893719 a 0 - 2 chr1 1011006 1013977 a 0 - 3 chr5 4944483 4950974 a 0 + 4 chr13 3817102 3821032 a 0 - 5 chr21 9687062 9694600 a 0 + 6 chr21 4060796 4068696 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfxo9wss2/f1.bed -b /tmp/tmpfxo9wss2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp86pxdehv/f1.bed -b /tmp/tmp86pxdehv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 368406 368407 a 0 + 1 chr1 2411140 2415512 a 0 - 2 chr2 4214711 4216809 a 0 - 3 chr19 3008649 3016037 a 0 - 4 chr19 5063230 5071461 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpeap92a7h/f1.bed -b /tmp/tmpeap92a7h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpezicejt0/f1.bed -b /tmp/tmpezicejt0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7075754 7081327 a 0 + 1 chr1 7741951 7745314 a 0 + 2 chr1 8442340 8449911 a 0 + 3 chr1 1 9773 a 0 + 4 chr1 6529851 6538562 a 0 + 5 chr1 4689685 4699457 a 0 + 6 chr1 831953 836191 a 0 + 7 chr2 2548933 2553184 a 0 + 8 chr9 1576414 1586414 a 0 + 9 chr19 6365121 6374893 a 0 + 10 chr20 6825928 6835700 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9jivry9m/f1.bed -b /tmp/tmp9jivry9m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3xrhx0oa/f1.bed -b /tmp/tmp3xrhx0oa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6185 a 0 + 1 chr1 1 6185 a 0 - 2 chr1 1 6185 a 0 - Chromosome Start End Name Score Strand 0 chr1 8294097 8295775 a 0 + 1 chr1 4782836 4789283 a 0 + 2 chr1 9344809 9353311 a 0 + 3 chr1 9999999 10004592 a 0 + 4 chr1 1238856 1248187 a 0 - 5 chr1 8470746 8480154 a 0 - 6 chr4 8470746 8475714 a 0 + 7 chr9 1663077 1671085 a 0 + 8 chr15 1364896 1368047 a 0 + 9 chr16 1859016 1868076 a 0 + 10 chrY 1407780 1415740 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwxl5fymj/f1.bed -b /tmp/tmpwxl5fymj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6185 a 0 + 1 chr1 1 6185 a 0 - 2 chr1 1 6185 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpg4gmqp75/f1.bed -b /tmp/tmpg4gmqp75/f2.bed Chromosome Start End Name Score Strand 0 chr1 4319860 4319861 a 0 + Chromosome Start End Name Score Strand 0 chr1 225 5537 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1bkzygcs/f1.bed -b /tmp/tmp1bkzygcs/f2.bed Chromosome Start End Name Score Strand 0 chr1 4319860 4319861 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqbkw5meo/f1.bed -b /tmp/tmpqbkw5meo/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 688731 691088 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmploeh891p/f1.bed -b /tmp/tmploeh891p/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4giymqx2/f1.bed -b /tmp/tmp4giymqx2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 9177 a 0 + 1 chr1 1 9177 a 0 - 2 chr1 1 9177 a 0 - Chromosome Start End Name Score Strand 0 chr1 5884153 5889707 a 0 + 1 chr1 6208538 6217508 a 0 - 2 chr1 6208538 6214644 a 0 - 3 chr1 3169785 3172900 a 0 - 4 chr3 6208538 6217946 a 0 - 5 chr13 6208538 6213106 a 0 + 6 chr18 6208538 6215765 a 0 - 7 chrX 6208538 6213946 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphm87oy9a/f1.bed -b /tmp/tmphm87oy9a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 9177 a 0 + 1 chr1 1 9177 a 0 - 2 chr1 1 9177 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0shbzxve/f1.bed -b /tmp/tmp0shbzxve/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 402778 410051 a 0 + 1 chr1 517430 517950 a 0 + 2 chr1 5208362 5214004 a 0 + 3 chr1 1601425 1610383 a 0 + 4 chr1 5420441 5427825 a 0 + 5 chr1 9474378 9482587 a 0 + 6 chr1 8625976 8634070 a 0 - 7 chr1 8883797 8887716 a 0 - 8 chr1 8828292 8838180 a 0 - 9 chr1 2781151 2787425 a 0 - 10 chr18 3401422 3411087 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4yq1e5zx/f1.bed -b /tmp/tmp4yq1e5zx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpstvpbn0m/f1.bed -b /tmp/tmpstvpbn0m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3539774 3545956 a 0 - 1 chr11 2881015 2891015 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjbaby5gf/f1.bed -b /tmp/tmpjbaby5gf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa3whebbf/f1.bed -b /tmp/tmpa3whebbf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6807 a 0 - 1 chr1 1 6807 a 0 - 2 chr1 1 6807 a 0 - Chromosome Start End Name Score Strand 0 chr1 4891979 4891980 a 0 + 1 chr1 4496000 4501306 a 0 + 2 chr1 382823 392291 a 0 + 3 chr1 4496000 4505468 a 0 + 4 chr1 4496000 4505735 a 0 - 5 chr6 10000000 10009549 a 0 + 6 chr6 4496000 4503495 a 0 - 7 chr7 4496000 4505468 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9dlnempg/f1.bed -b /tmp/tmp9dlnempg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6807 a 0 - 1 chr1 1 6807 a 0 - 2 chr1 1 6807 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmph_msvp4_/f1.bed -b /tmp/tmph_msvp4_/f2.bed Chromosome Start End Name Score Strand 0 chr17 1 2 a 0 + 1 chr17 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 3333332 3338469 a 0 + 1 chr14 4935379 4940516 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8o5fqs2d/f1.bed -b /tmp/tmp8o5fqs2d/f2.bed Chromosome Start End Name Score Strand 0 chr17 1 2 a 0 + 1 chr17 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp279bggct/f1.bed -b /tmp/tmp279bggct/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 1980260 1981051 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwsqadjrt/f1.bed -b /tmp/tmpwsqadjrt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfi92zw_y/f1.bed -b /tmp/tmpfi92zw_y/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr7 2482570 2483120 a 0 + 1 chr8 1003293 1003843 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpcvrq4jus/f1.bed -b /tmp/tmpcvrq4jus/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpsoi6kq0v/f1.bed -b /tmp/tmpsoi6kq0v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6670 a 0 + 1 chr1 1 6670 a 0 - Chromosome Start End Name Score Strand 0 chr1 6931542 6939714 a 0 + 1 chr1 2006215 2010514 a 0 - 2 chr1 7868849 7869702 a 0 - 3 chr4 8004907 8010869 a 0 - 4 chr8 5509878 5518792 a 0 + 5 chr13 962734 965744 a 0 - 6 chr14 7435178 7438042 a 0 - 7 chr21 9627601 9636515 a 0 + 8 chr22 8862951 8872325 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpb7s3izbg/f1.bed -b /tmp/tmpb7s3izbg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6670 a 0 + 1 chr1 1 6670 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplr51fl4s/f1.bed -b /tmp/tmplr51fl4s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwj5g74td/f1.bed -b /tmp/tmpwj5g74td/f2.bed ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain53-method_chain53] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 174 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________ test_k_nearest[upstream-False-opposite-last] _________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 769 | 2050 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 43 | 1837 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RQZc9hAAFGBmYGBiZWECuRI+EMkA+CXAwMWkCKnx3CBQBFNwKM') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY0zkSDjDgAIYGRkwAQA7AAGZ') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz3zg8vot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3zg8vot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpauiiru2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpauiiru2z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3at6qccl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3at6qccl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9qpxpioo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qpxpioo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpibr39c5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibr39c5i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5cjr6jor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5cjr6jor/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbt02cen8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt02cen8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnwevakal/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwevakal/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0se4w13h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0se4w13h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp231bavdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp231bavdq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmzv99vv3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzv99vv3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdf917koo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf917koo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprz0lmlto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprz0lmlto/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl_az50gl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_az50gl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptv6yt4kz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv6yt4kz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbwfixqz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbwfixqz3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4dbcscbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dbcscbc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcj8mm5iv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcj8mm5iv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcpho1lgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcpho1lgf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp385km3n6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp385km3n6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdlo8zdvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlo8zdvk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3lf5gooi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3lf5gooi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9ad7t34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9ad7t34/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpshldoxer/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshldoxer/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp57l72o8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57l72o8c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplhzy_6kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplhzy_6kr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3fvriyx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3fvriyx7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz030p8it/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz030p8it/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptg3p6uk1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptg3p6uk1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq62v3n8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq62v3n8n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprfkmsc7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprfkmsc7s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprcu69awe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcu69awe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfcs15d0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcs15d0h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4q3udovi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4q3udovi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph0glpx4f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph0glpx4f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph4xszik2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4xszik2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppi69hi5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppi69hi5b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp813vjfus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp813vjfus/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpihphnm8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihphnm8k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpym0m7t_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpym0m7t_q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm_oh584o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_oh584o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdbx_nins/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbx_nins/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd2cy4_jn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2cy4_jn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8u6kxz9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8u6kxz9m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl6wcz6r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6wcz6r6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmxcbv78g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxcbv78g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwkgnmruy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwkgnmruy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe39fd_v_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe39fd_v_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4avi1nmj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4avi1nmj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_nwkvq5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_nwkvq5g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmzreae_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzreae_8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmoo12j2o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmoo12j2o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy6mxut1x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6mxut1x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl9vjlief/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9vjlief/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpigpnzeyi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigpnzeyi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6tgemw8z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6tgemw8z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3xfb_ry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3xfb_ry/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnmuuo2mk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmuuo2mk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_nu_vu5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_nu_vu5w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc1olz093/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1olz093/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ihvo3m6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ihvo3m6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjogsndt8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjogsndt8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk8c82zb4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8c82zb4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxxwih5w7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxwih5w7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf6r19fg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf6r19fg4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8prqgrr9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8prqgrr9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1ol1_3s9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ol1_3s9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp68lcqwwf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68lcqwwf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqo8em30d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqo8em30d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy8socne9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy8socne9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7pnqq9ux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pnqq9ux/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuwpobm2k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwpobm2k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk113n1l1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk113n1l1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnpf83vbs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnpf83vbs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6tl5viad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6tl5viad/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9es79m1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9es79m1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfo52js4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfo52js4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdkjsjhvc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkjsjhvc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpey653h45/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpey653h45/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm3mw9cea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3mw9cea/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp05upy6f0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05upy6f0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpebuiohld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebuiohld/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_coverage[same] ______________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpp7p2dvru/f1.bed -b /tmp/tmpp7p2dvru/f2.bed Chromosome Start End Name Score Strand 0 chr1 2600664 2602048 a 0 + 1 chr1 4063062 4072875 a 0 + 2 chr1 8599245 8609136 a 0 + 3 chr8 1 6831 a 0 - Chromosome Start End Name Score Strand 0 chr1 10000000 10000830 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2lfkzg3h/f1.bed -b /tmp/tmp2lfkzg3h/f2.bed Chromosome Start End Name Score Strand 0 chr1 2600664 2602048 a 0 + 1 chr1 4063062 4072875 a 0 + 2 chr1 8599245 8609136 a 0 + 3 chr2 1 6831 a 0 - Chromosome Start End Name Score Strand 0 chr1 10000000 10000830 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2bzpwpqm/f1.bed -b /tmp/tmp2bzpwpqm/f2.bed Chromosome Start End Name Score Strand 0 chr1 2600664 2602048 a 0 + 1 chr1 4063062 4072875 a 0 + 2 chr1 8599245 8609136 a 0 + 3 chr2 1 6831 a 0 - Chromosome Start End Name Score Strand 0 chr1 2600664 2602048 a 0 + 1 chr1 4063062 4072875 a 0 + 2 chr1 8599245 8609136 a 0 + 3 chr2 1 6831 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp862f6ul0/f1.bed -b /tmp/tmp862f6ul0/f2.bed Chromosome Start End Name Score Strand 0 chr1 2600664 2600929 a 0 + 1 chr1 4063062 4071570 a 0 + 2 chr1 8599245 8600015 a 0 + 3 chr2 1 5634 a 0 + Chromosome Start End Name Score Strand 0 chr1 1523171 1523461 a 0 + 1 chr1 2600664 2602714 a 0 + 2 chr1 2917175 2921789 a 0 + 3 chr1 2917175 2925903 a 0 - 4 chr2 11 5135 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4ogb7fhu/f1.bed -b /tmp/tmp4ogb7fhu/f2.bed Chromosome Start End Name Score Strand 0 chr1 2600664 2600929 a 0 + 1 chr1 4063062 4071570 a 0 + 2 chr1 8599245 8600015 a 0 + 3 chr2 1 5634 a 0 + Chromosome Start End Name Score Strand 0 chr1 1523171 1523175 a 0 + 1 chr1 1523171 1529084 a 0 - 2 chr1 1523171 1523943 a 0 - 3 chr1 1523171 1523197 a 0 - 4 chr2 1441794 1449480 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd0swac1t/f1.bed -b /tmp/tmpd0swac1t/f2.bed Chromosome Start End Name Score Strand 0 chr1 2600664 2600929 a 0 + 1 chr1 4063062 4071570 a 0 + 2 chr1 8599245 8600015 a 0 + 3 chr2 1 5634 a 0 + Chromosome Start End Name Score Strand 0 chr1 851987 851991 a 0 + 1 chr1 1442561 1448474 a 0 - 2 chr1 1288 2060 a 0 - 3 chr1 1288 1314 a 0 - 4 chr2 1288 1314 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp68vyjzse/f1.bed -b /tmp/tmp68vyjzse/f2.bed Chromosome Start End Name Score Strand 0 chr1 131355 131613 a 0 + 1 chr1 196610 196868 a 0 + 2 chr1 1704194 1704452 a 0 - 3 chr2 196610 196868 a 0 - Chromosome Start End Name Score Strand 0 chr1 7209331 7209346 a 0 + 1 chr1 2 2033 a 0 + 2 chr1 7153290 7159948 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsazudftz/f1.bed -b /tmp/tmpsazudftz/f2.bed Chromosome Start End Name Score Strand 0 chr1 2473427 2478436 a 0 + 1 chr1 9935374 9943486 a 0 + 2 chr1 9935374 9936873 a 0 + 3 chr1 9935374 9943918 a 0 - 4 chr1 9935374 9943960 a 0 - 5 chr4 7559629 7567910 a 0 + 6 chr4 9935374 9943320 a 0 - 7 chr8 1445638 1448264 a 0 - 8 chr8 1489049 1490229 a 0 - 9 chr10 196914 200456 a 0 + 10 chr17 9935374 9935649 a 0 + Chromosome Start End Name Score Strand 0 chr1 7229883 7238666 a 0 - 1 chr4 6141350 6143794 a 0 + 2 chr4 4421984 4426364 a 0 - 3 chr19 9717012 9726328 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_0xst0kb/f1.bed -b /tmp/tmp_0xst0kb/f2.bed Chromosome Start End Name Score Strand 0 chr1 2473427 2478436 a 0 + 1 chr1 9935374 9943486 a 0 + 2 chr1 9935374 9936873 a 0 + 3 chr1 9935374 9943918 a 0 - 4 chr1 9935374 9943960 a 0 - 5 chr4 7559629 7567910 a 0 + 6 chr4 9935374 9943320 a 0 - 7 chr8 1445638 1448264 a 0 - 8 chr8 1489049 1490229 a 0 - 9 chr10 196914 200456 a 0 + 10 chr17 9935374 9935649 a 0 + Chromosome Start End Name Score Strand 0 chr1 7229883 7238666 a 0 - 1 chr4 6141350 6143794 a 0 + 2 chr4 4421984 4426364 a 0 - 3 chr19 9717012 9726328 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi0geoan1/f1.bed -b /tmp/tmpi0geoan1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdny8401p/f1.bed -b /tmp/tmpdny8401p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_l0gt_bf/f1.bed -b /tmp/tmp_l0gt_bf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpogswew09/f1.bed -b /tmp/tmpogswew09/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpra_tfqbt/f1.bed -b /tmp/tmpra_tfqbt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkmwr2gag/f1.bed -b /tmp/tmpkmwr2gag/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfz44lu4c/f1.bed -b /tmp/tmpfz44lu4c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppvjh07oz/f1.bed -b /tmp/tmppvjh07oz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn724jvbe/f1.bed -b /tmp/tmpn724jvbe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2itkma57/f1.bed -b /tmp/tmp2itkma57/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppql18cb_/f1.bed -b /tmp/tmppql18cb_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8fuhhjy5/f1.bed -b /tmp/tmp8fuhhjy5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpeh_qokew/f1.bed -b /tmp/tmpeh_qokew/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpm2kni_7e/f1.bed -b /tmp/tmpm2kni_7e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpon9wlk20/f1.bed -b /tmp/tmpon9wlk20/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxeqabajl/f1.bed -b /tmp/tmpxeqabajl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmdbuma2i/f1.bed -b /tmp/tmpmdbuma2i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2wcuyvkt/f1.bed -b /tmp/tmp2wcuyvkt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu7ir63fn/f1.bed -b /tmp/tmpu7ir63fn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp08suu7lr/f1.bed -b /tmp/tmp08suu7lr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7y0ekyx6/f1.bed -b /tmp/tmp7y0ekyx6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj48aqo5k/f1.bed -b /tmp/tmpj48aqo5k/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy7j0j8zm/f1.bed -b /tmp/tmpy7j0j8zm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvnsltfm7/f1.bed -b /tmp/tmpvnsltfm7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi4135jk_/f1.bed -b /tmp/tmpi4135jk_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpm3p4exiu/f1.bed -b /tmp/tmpm3p4exiu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8ci8udik/f1.bed -b /tmp/tmp8ci8udik/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0u5fxjkh/f1.bed -b /tmp/tmp0u5fxjkh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5751060 5751062 a 0 + 1 chr1 3397027 3403561 a 0 + 2 chr1 2649157 2651947 a 0 + 3 chr1 4209962 4216108 a 0 - 4 chr1 7097319 7099763 a 0 - 5 chrX 3654488 3654812 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpadgu15ic/f1.bed -b /tmp/tmpadgu15ic/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvvomfr60/f1.bed -b /tmp/tmpvvomfr60/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 6048266 6048480 a 0 - 1 chr7 9556010 9561061 a 0 + 2 chr13 9256101 9260081 a 0 + 3 chr22 3117446 3120147 a 0 + 4 chr22 7572310 7579254 a 0 - 5 chrY 7832432 7839749 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpoasi1073/f1.bed -b /tmp/tmpoasi1073/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuwl7_4iu/f1.bed -b /tmp/tmpuwl7_4iu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr10 1299733 1303073 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdl4a9i8n/f1.bed -b /tmp/tmpdl4a9i8n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2povvq00/f1.bed -b /tmp/tmp2povvq00/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3712169 3714519 a 0 + 1 chr1 4944430 4951591 a 0 - 2 chr4 4347415 4352780 a 0 - 3 chr7 293497 299892 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplomv6c2w/f1.bed -b /tmp/tmplomv6c2w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7baenmmw/f1.bed -b /tmp/tmp7baenmmw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4963409 4963491 a 0 + 1 chr1 7462727 7464546 a 0 + 2 chr1 10000000 10008748 a 0 + 3 chr1 1045798 1051992 a 0 - 4 chr1 795051 797008 a 0 - 5 chr1 6880214 6885790 a 0 - 6 chr4 3242946 3248003 a 0 + 7 chr4 438731 444647 a 0 - 8 chr4 6354894 6357355 a 0 - 9 chr19 2966409 2974438 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpphk5slom/f1.bed -b /tmp/tmpphk5slom/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgpyiag50/f1.bed -b /tmp/tmpgpyiag50/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 694013 702112 a 0 + 1 chr1 6797927 6799591 a 0 + 2 chr1 5629118 5638368 a 0 - 3 chr1 217070 226880 a 0 - 4 chr5 8726938 8730008 a 0 - 5 chr6 1545404 1546921 a 0 + 6 chr6 8991880 8999419 a 0 - 7 chr8 6399677 6401599 a 0 + 8 chr10 5152951 5156709 a 0 + 9 chr16 3712961 3712962 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuw_2y26b/f1.bed -b /tmp/tmpuw_2y26b/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvat70gs6/f1.bed -b /tmp/tmpvat70gs6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7878354 7878490 a 0 + 1 chr1 1925883 1929345 a 0 - 2 chr2 8472938 8479453 a 0 + 3 chr6 4938944 4938945 a 0 + 4 chr14 1 757 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp__1urii8/f1.bed -b /tmp/tmp__1urii8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpat_ef0z4/f1.bed -b /tmp/tmpat_ef0z4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr16 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7810494 7818184 a 0 + 1 chr1 6917839 6918572 a 0 + 2 chr1 6917839 6918421 a 0 - 3 chr8 1076161 1084136 a 0 - 4 chr15 6917839 6923167 a 0 - 5 chr16 1394633 1402535 a 0 + 6 chr16 6917839 6922894 a 0 - 7 chrY 6917839 6922300 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvv85v4u5/f1.bed -b /tmp/tmpvv85v4u5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr16 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc540f_c9/f1.bed -b /tmp/tmpc540f_c9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 8335 a 0 + 1 chr1 1 8335 a 0 - 2 chr1 1 8335 a 0 - Chromosome Start End Name Score Strand 0 chr1 3348662 3352488 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8wkexgta/f1.bed -b /tmp/tmp8wkexgta/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 8335 a 0 + 1 chr1 1 8335 a 0 - 2 chr1 1 8335 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsmh5olku/f1.bed -b /tmp/tmpsmh5olku/f2.bed Chromosome Start End Name Score Strand 0 chr1 4867054 4867055 a 0 + Chromosome Start End Name Score Strand 0 chr1 13340 21532 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc8cprsim/f1.bed -b /tmp/tmpc8cprsim/f2.bed Chromosome Start End Name Score Strand 0 chr1 4867054 4867055 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp84kq9p3p/f1.bed -b /tmp/tmp84kq9p3p/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65539 a 0 + Chromosome Start End Name Score Strand 0 chr1 3172411 3175871 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa9z08a9q/f1.bed -b /tmp/tmpa9z08a9q/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65539 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxla5xshp/f1.bed -b /tmp/tmpxla5xshp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 8529 a 0 + 1 chr1 1 8529 a 0 - Chromosome Start End Name Score Strand 0 chr1 2 131 a 0 + 1 chr1 8561057 8561186 a 0 - 2 chr2 9999999 10006784 a 0 + 3 chr2 1163792 1166951 a 0 - 4 chr5 9934299 9935586 a 0 - 5 chr7 1889088 1889217 a 0 + 6 chr10 6138778 6147288 a 0 - 7 chr13 9407363 9407492 a 0 - 8 chr16 6591596 6593640 a 0 + 9 chr18 2016133 2016262 a 0 + 10 chr21 7482691 7482820 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpas_qo53n/f1.bed -b /tmp/tmpas_qo53n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 8529 a 0 + 1 chr1 1 8529 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4zjfx3g0/f1.bed -b /tmp/tmp4zjfx3g0/f2.bed Chromosome Start End Name Score Strand 0 chr13 1 258 a 0 + Chromosome Start End Name Score Strand 0 chr2 2 9146 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcdecy8d9/f1.bed -b /tmp/tmpcdecy8d9/f2.bed Chromosome Start End Name Score Strand 0 chr13 1 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp859ae0ug/f1.bed -b /tmp/tmp859ae0ug/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4381736 4391431 a 0 + 1 chr15 9387110 9394368 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwvs0gw_l/f1.bed -b /tmp/tmpwvs0gw_l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzomi43qm/f1.bed -b /tmp/tmpzomi43qm/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6253913 6261743 a 0 + 1 chr1 1585496 1588327 a 0 + 2 chr1 8896372 8900480 a 0 + 3 chr11 8011892 8020729 a 0 + 4 chr14 7000885 7001413 a 0 + 5 chr16 7279961 7281654 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4qbvxtfp/f1.bed -b /tmp/tmp4qbvxtfp/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmph4uhmieo/f1.bed -b /tmp/tmph4uhmieo/f2.bed Chromosome Start End Name Score Strand 0 chr12 1 258 a 0 + Chromosome Start End Name Score Strand 0 chr6 8838107 8840624 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpag8e_6ln/f1.bed -b /tmp/tmpag8e_6ln/f2.bed Chromosome Start End Name Score Strand 0 chr12 1 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9fbf1bek/f1.bed -b /tmp/tmp9fbf1bek/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8714730 8718967 a 0 + 1 chr1 9832024 9839325 a 0 + 2 chr1 7311708 7313720 a 0 + 3 chr1 7715690 7725690 a 0 + 4 chr1 8161231 8161232 a 0 + 5 chr1 8009343 8016613 a 0 - 6 chr1 532796 535552 a 0 - 7 chr7 8627523 8628148 a 0 + 8 chr10 6453829 6459471 a 0 - 9 chr15 10000000 10000625 a 0 - 10 chrX 3969356 3975635 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprau5ovgo/f1.bed -b /tmp/tmprau5ovgo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqbs_bwy_/f1.bed -b /tmp/tmpqbs_bwy_/f2.bed Chromosome Start End Name Score Strand 0 chr21 1380664 1380665 a 0 - Chromosome Start End Name Score Strand 0 chr1 4888114 4897525 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdpfxcaut/f1.bed -b /tmp/tmpdpfxcaut/f2.bed Chromosome Start End Name Score Strand 0 chr21 1380664 1380665 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsxq7h64c/f1.bed -b /tmp/tmpsxq7h64c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8587485 8588393 a 0 + 1 chr1 7941369 7941394 a 0 + 2 chr1 8196095 8197499 a 0 - 3 chr8 1 6247 a 0 + 4 chr11 1424278 1426569 a 0 + 5 chr11 3411413 3416801 a 0 - 6 chr22 8304789 8308821 a 0 + 7 chr22 10000000 10007572 a 0 + 8 chr22 3071908 3078376 a 0 + 9 chr22 9150213 9150733 a 0 + 10 chr22 8601694 8608336 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphp7nhqmm/f1.bed -b /tmp/tmphp7nhqmm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3l4m1aeq/f1.bed -b /tmp/tmp3l4m1aeq/f2.bed Chromosome Start End Name Score Strand 0 chr1 7643041 7643042 a 0 + Chromosome Start End Name Score Strand 0 chr1 183 7429 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplw49ljq8/f1.bed -b /tmp/tmplw49ljq8/f2.bed Chromosome Start End Name Score Strand 0 chr1 7643041 7643042 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgb_9oklo/f1.bed -b /tmp/tmpgb_9oklo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 127 a 0 + 1 chr1 1 127 a 0 + 2 chr1 1 127 a 0 - Chromosome Start End Name Score Strand 0 chr1 10000000 10007481 a 0 - 1 chr1 3098351 3101868 a 0 - 2 chr1 3425563 3428579 a 0 - 3 chr1 2986071 2987115 a 0 - 4 chr3 3079468 3082798 a 0 - 5 chr7 3696557 3696558 a 0 - 6 chr7 6094407 6094888 a 0 - 7 chr10 4226746 4229983 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppz069hsh/f1.bed -b /tmp/tmppz069hsh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 127 a 0 + 1 chr1 1 127 a 0 + 2 chr1 1 127 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcjk4h_yv/f1.bed -b /tmp/tmpcjk4h_yv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 140758 150713 a 0 + 1 chr1 6774460 6783695 a 0 + 2 chr1 4199885 4208571 a 0 + 3 chr1 7269424 7278913 a 0 + 4 chr1 6283165 6283746 a 0 - 5 chr1 7361129 7364611 a 0 - 6 chr1 1201304 1209792 a 0 - 7 chr1 481640 491292 a 0 - 8 chr1 645920 647031 a 0 - 9 chr1 7361129 7367946 a 0 - 10 chrM 3237976 3241999 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp74un2ifr/f1.bed -b /tmp/tmp74un2ifr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp40656wts/f1.bed -b /tmp/tmp40656wts/f2.bed Chromosome Start End Name Score Strand 0 chr1 4820344 4820345 a 0 + Chromosome Start End Name Score Strand 0 chr1 80 3804 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphc022i7t/f1.bed -b /tmp/tmphc022i7t/f2.bed Chromosome Start End Name Score Strand 0 chr1 4820344 4820345 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa53k6zp0/f1.bed -b /tmp/tmpa53k6zp0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 323471 324137 a 0 + 1 chr1 5999646 6006033 a 0 - 2 chr1 831742 835528 a 0 - 3 chr7 8652916 8657984 a 0 + 4 chr15 5475104 5482905 a 0 + 5 chr19 7839153 7849046 a 0 - 6 chr21 9108583 9115901 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp93juckxa/f1.bed -b /tmp/tmp93juckxa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsvzs_qdr/f1.bed -b /tmp/tmpsvzs_qdr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9773469 9777258 a 0 + 1 chr1 10000000 10004068 a 0 + 2 chr1 1838769 1839101 a 0 + 3 chr1 5033228 5043102 a 0 + 4 chr1 2054964 2063203 a 0 + 5 chr1 7211253 7213915 a 0 - 6 chr6 7960168 7963848 a 0 - 7 chr10 2033697 2043665 a 0 - 8 chr12 412331 417057 a 0 - 9 chrM 2473116 2480421 a 0 + 10 chrX 3026397 3029395 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2yiaybmt/f1.bed -b /tmp/tmp2yiaybmt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe48x4gyn/f1.bed -b /tmp/tmpe48x4gyn/f2.bed Chromosome Start End Name Score Strand 0 chrY 1 2 a 0 + 1 chrY 6190594 6190595 a 0 + Chromosome Start End Name Score Strand 0 chr16 2 9892 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3o9cnssz/f1.bed -b /tmp/tmp3o9cnssz/f2.bed Chromosome Start End Name Score Strand 0 chrY 1 2 a 0 + 1 chrY 6190594 6190595 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo42bvtme/f1.bed -b /tmp/tmpo42bvtme/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4411379 4412939 a 0 + 1 chr1 4429164 4433606 a 0 - 2 chr1 8791329 8800216 a 0 - 3 chr17 3977088 3981826 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe6_dncu7/f1.bed -b /tmp/tmpe6_dncu7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpstgwey9q/f1.bed -b /tmp/tmpstgwey9q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 3183 a 0 + 1 chr1 1 3183 a 0 - Chromosome Start End Name Score Strand 0 chr1 6659878 6666753 a 0 + 1 chr1 1198728 1208590 a 0 + 2 chr1 6430830 6435797 a 0 - 3 chr6 9021685 9024418 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplghiq9hn/f1.bed -b /tmp/tmplghiq9hn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 3183 a 0 + 1 chr1 1 3183 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc1w7glm5/f1.bed -b /tmp/tmpc1w7glm5/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr2 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr22 6845173 6847305 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmqu0we1a/f1.bed -b /tmp/tmpmqu0we1a/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr2 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5lc1xzr7/f1.bed -b /tmp/tmp5lc1xzr7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr3 2420723 2426383 a 0 + 1 chr16 6583788 6587098 a 0 + 2 chr16 518044 518790 a 0 + 3 chr16 2 641 a 0 + 4 chr16 1057639 1064881 a 0 - 5 chr16 5189138 5197825 a 0 - 6 chr16 1150952 1153395 a 0 - 7 chr16 5796851 5803858 a 0 - 8 chr16 3481988 3485679 a 0 - 9 chr16 2333345 2339704 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcrr5tzzq/f1.bed -b /tmp/tmpcrr5tzzq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpt79fmcqp/f1.bed -b /tmp/tmpt79fmcqp/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65539 a 0 + Chromosome Start End Name Score Strand 0 chr1 4684842 4686880 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2n5kvasf/f1.bed -b /tmp/tmp2n5kvasf/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65539 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpikxv8ayi/f1.bed -b /tmp/tmpikxv8ayi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9771151 9771562 a 0 - 1 chr1 1048567 1048568 a 0 - 2 chr2 8812345 8813401 a 0 - 3 chr21 5758758 5758956 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp92v9_ov3/f1.bed -b /tmp/tmp92v9_ov3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_u0g1f68/f1.bed -b /tmp/tmp_u0g1f68/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 490434 496485 a 0 + 1 chr1 9010921 9016972 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6ox62s7f/f1.bed -b /tmp/tmp6ox62s7f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqtbmmkvw/f1.bed -b /tmp/tmpqtbmmkvw/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6968729 6973690 a 0 + 1 chr1 6968729 6975133 a 0 + 2 chr1 6968729 6976636 a 0 - 3 chr1 6968729 6975649 a 0 - 4 chr1 6968729 6973258 a 0 - 5 chr2 6968729 6975010 a 0 + 6 chr7 4593336 4598816 a 0 - 7 chr9 6968729 6977547 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvmd09ew4/f1.bed -b /tmp/tmpvmd09ew4/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa0wmoxln/f1.bed -b /tmp/tmpa0wmoxln/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 232 a 0 + 1 chr1 1 232 a 0 - Chromosome Start End Name Score Strand 0 chr1 1336112 1341335 a 0 + 1 chr1 7114248 7117217 a 0 + 2 chr1 4591164 4595488 a 0 + 3 chr1 6770484 6778960 a 0 + 4 chr1 4024139 4024608 a 0 + 5 chr1 4143764 4143859 a 0 - 6 chr2 7244529 7246215 a 0 + 7 chr9 1334393 1336848 a 0 + 8 chr11 8181329 8187793 a 0 + 9 chr11 3369774 3374098 a 0 + 10 chrY 5166599 5176405 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj8yywk2e/f1.bed -b /tmp/tmpj8yywk2e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 232 a 0 + 1 chr1 1 232 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk3lznb82/f1.bed -b /tmp/tmpk3lznb82/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4874663 4878614 a 0 + 1 chr1 6928962 6932913 a 0 + 2 chr1 6010494 6016365 a 0 + 3 chr1 530525 534215 a 0 - 4 chr4 9315443 9323073 a 0 + 5 chr4 8235864 8235894 a 0 - 6 chr8 6878948 6881187 a 0 + 7 chr19 4988512 4992463 a 0 + 8 chrY 2545153 2547884 a 0 + 9 chrY 9765886 9767122 a 0 + 10 chrY 551818 554984 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6fqw3qi2/f1.bed -b /tmp/tmp6fqw3qi2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpyc5flh7e/f1.bed -b /tmp/tmpyc5flh7e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp754jlf_m/f1.bed -b /tmp/tmp754jlf_m/f2.bed ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain21-method_chain21] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 6403 | 6454 | a | 0 | + | | | chr1 | 1507856 | 1507907 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 6403 | 8722 | a | 0 | + | | | chr1 | 2332 | 4651 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 179 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY+FUSvvIalQTacoABGwMjAySTAzM4kz8DCIMRswMDBwMPEAxBgYWkBJGz4TGLgZmRka4Uk7G6A+rtzJwSjMwOHPygYxgkBECGgCkAeiFCfU=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr7 | 6403 | 6680 | a | 0 | + | | | chr7 | 6403 | 6680 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1075 | 1405 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 133378 | 135710 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 271 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY1FK+8jKVDNjWj0DAwMbAyODJBMDM6MIByMDO5DDwmDEzMDAwQABLEY8DKaMnkBxBgZGIAALgnRwApnapgyc0gwMAE2DBao=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain54-method_chain54] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3.12/typing.py:1176 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_k_nearest[upstream-False-same-last] ___________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 258 | a | 0 | + | | | chr1 | 1 | 258 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2050 | 5635 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAAsZ4BkY9BgRgBEMGRrWganYQj5WBg5EhgA/IBAApmgH9') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5eaojszq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5eaojszq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphg1oito3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphg1oito3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9yl3m_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9yl3m_4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjan3qatk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjan3qatk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmvk_qscl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvk_qscl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuiqpfg9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuiqpfg9_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyl8ldvtd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyl8ldvtd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ti1b0qp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ti1b0qp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0c9v8oqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0c9v8oqd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuh_u38p8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuh_u38p8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdla_tdkg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdla_tdkg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw7emfbr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7emfbr4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpegiohhl3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegiohhl3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5y3l0fg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5y3l0fg6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpenmll1i3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenmll1i3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr1qprvos/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1qprvos/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl2yrmt3e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl2yrmt3e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdvt9z2i4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdvt9z2i4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfi05kg12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfi05kg12/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnv2htogv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnv2htogv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpld9n3_yr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpld9n3_yr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps9zbzj3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9zbzj3j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuh6ew44c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuh6ew44c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfcmj69zm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcmj69zm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5zckoy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5zckoy8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3e53v9b7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3e53v9b7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcrqbiu8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcrqbiu8a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpylvlpocc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpylvlpocc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjxx65uq1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxx65uq1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2dzk0723/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dzk0723/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplbdv1_s2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbdv1_s2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0vnl9qi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0vnl9qi6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdt41191w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt41191w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjqs_niyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqs_niyj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmh7llx1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmh7llx1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkpkmpjz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkpkmpjz7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsk47uer5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsk47uer5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpepsk780w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepsk780w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4_zo5fk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4_zo5fk6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpooo85ze8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpooo85ze8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9u3lvkmj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9u3lvkmj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnnkw_fdd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnnkw_fdd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcsn171p7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcsn171p7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp99scnpu5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99scnpu5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8dnyh0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8dnyh0k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_pt9r08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_pt9r08/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi9wp1uhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi9wp1uhy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1vwg2ndd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vwg2ndd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoh7svah3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoh7svah3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwmyz6upy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmyz6upy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_1dwevk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_1dwevk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8vxk80ec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8vxk80ec/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphjlqry3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjlqry3k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppw1h34xn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppw1h34xn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclepsuzh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclepsuzh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv0yrxqby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv0yrxqby/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcngsh_qt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcngsh_qt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp700lp1_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp700lp1_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ggvpxrm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ggvpxrm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6n__e8pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6n__e8pb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4sbc9qzs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4sbc9qzs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkv7kz9xe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkv7kz9xe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl7c65_rp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7c65_rp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbpploxtw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpploxtw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpss04rx58/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpss04rx58/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3x80zrx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3x80zrx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppiakp8au/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppiakp8au/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9qcfng37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qcfng37/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzedfbszd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzedfbszd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5weud5rs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5weud5rs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr679infd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr679infd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp07qg76cj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07qg76cj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb4sos98k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb4sos98k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphv0qesah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphv0qesah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxyb91c47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxyb91c47/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbgnjbp9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgnjbp9j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3h8jj5c8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3h8jj5c8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp27v8sq9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp27v8sq9y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy8_d1wmj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy8_d1wmj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8hub4wv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hub4wv7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphf78mk36/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphf78mk36/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplwy8lli1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwy8lli1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7ke9k_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7ke9k_9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2_4yrl4d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2_4yrl4d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmbyo4v35/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbyo4v35/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppemqt_6c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppemqt_6c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc_d2khq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_d2khq7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7hevkd8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7hevkd8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp409_8f_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp409_8f_v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqub5sily/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqub5sily/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprxthol72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxthol72/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ps6pm7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ps6pm7q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpenewwjpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenewwjpl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4zws7adv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zws7adv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmzmaeiyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzmaeiyy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3_i6hvfs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_i6hvfs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwjsltv4w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjsltv4w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplw5_a7ei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplw5_a7ei/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk5u7r_hm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5u7r_hm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxgt_sx5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgt_sx5i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_v6kw4x6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_v6kw4x6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmperuc3jk0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmperuc3jk0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn451vyxm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn451vyxm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiio8jqdl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiio8jqdl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn73pzv8i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn73pzv8i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7ru2uqmt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ru2uqmt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmqxnzkhx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqxnzkhx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7y0s426/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7y0s426/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpown9bqvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpown9bqvk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfqwb5pt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfqwb5pt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph4jvsnj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4jvsnj1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxenq7ot_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxenq7ot_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcs3gizi0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcs3gizi0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7b9w9usa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7b9w9usa/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________________ test_coverage[opposite] ____________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphb2ugd5w/f1.bed -b /tmp/tmphb2ugd5w/f2.bed Chromosome Start End Name Score Strand 0 chr1 8360190 8366346 a 0 - Chromosome Start End Name Score Strand 0 chr19 6079463 6089462 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpx1u2sigz/f1.bed -b /tmp/tmpx1u2sigz/f2.bed Chromosome Start End Name Score Strand 0 chr1 8360190 8366346 a 0 - Chromosome Start End Name Score Strand 0 chr19 8360190 8370189 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmknvq2o4/f1.bed -b /tmp/tmpmknvq2o4/f2.bed Chromosome Start End Name Score Strand 0 chr1 8360190 8368292 a 0 + Chromosome Start End Name Score Strand 0 chr5 3073 3842 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5sq1jsj5/f1.bed -b /tmp/tmp5sq1jsj5/f2.bed Chromosome Start End Name Score Strand 0 chr1 8360190 8368292 a 0 + Chromosome Start End Name Score Strand 0 chr1 8360190 8368292 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpl9p17vsk/f1.bed -b /tmp/tmpl9p17vsk/f2.bed Chromosome Start End Name Score Strand 0 chr1 8360190 8368292 a 0 + Chromosome Start End Name Score Strand 0 chr1 9501953 9510055 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3gfmrhm8/f1.bed -b /tmp/tmp3gfmrhm8/f2.bed Chromosome Start End Name Score Strand 0 chr1 8360190 8368292 a 0 + Chromosome Start End Name Score Strand 0 chr1 4896 5153 a 0 + 1 chr1 4896 6623 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsx_x0oor/f1.bed -b /tmp/tmpsx_x0oor/f2.bed Chromosome Start End Name Score Strand 0 chr1 24352 24354 a 0 + 1 chr1 24352 33562 a 0 - Chromosome Start End Name Score Strand 0 chr1 5430751 5440750 a 0 + 1 chr7 5430751 5431817 a 0 + 2 chr7 5430751 5440751 a 0 + 3 chr7 5430751 5431216 a 0 + 4 chr7 3330 12361 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbohrtjt_/f1.bed -b /tmp/tmpbohrtjt_/f2.bed Chromosome Start End Name Score Strand 0 chr1 9581236 9583876 a 0 - 1 chr1 4638460 4640356 a 0 - 2 chr1 6263089 6265006 a 0 - 3 chr9 4383691 4386085 a 0 - 4 chr17 786152 793206 a 0 - 5 chr18 3318895 3319518 a 0 + 6 chr20 1 4145 a 0 - 7 chrX 1 3195 a 0 - Chromosome Start End Name Score Strand 0 chr1 7622338 7622921 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphs21a772/f1.bed -b /tmp/tmphs21a772/f2.bed Chromosome Start End Name Score Strand 0 chr1 9581236 9583876 a 0 - 1 chr1 4638460 4640356 a 0 - 2 chr1 6263089 6265006 a 0 - 3 chr9 4383691 4386085 a 0 - 4 chr17 786152 793206 a 0 - 5 chr18 3318895 3319518 a 0 + 6 chr20 1 4145 a 0 - 7 chrX 1 3195 a 0 - Chromosome Start End Name Score Strand 0 chr1 9581236 9583876 a 0 - 1 chr1 4638460 4640356 a 0 - 2 chr1 6263089 6265006 a 0 - 3 chr9 4383691 4386085 a 0 - 4 chr17 786152 793206 a 0 - 5 chr18 3318895 3319518 a 0 + 6 chr20 1 4145 a 0 - 7 chrX 1 3195 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzq6ro68l/f1.bed -b /tmp/tmpzq6ro68l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5rv5jg6s/f1.bed -b /tmp/tmp5rv5jg6s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpokegy1zo/f1.bed -b /tmp/tmpokegy1zo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzdvdppdj/f1.bed -b /tmp/tmpzdvdppdj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpay_pswq_/f1.bed -b /tmp/tmpay_pswq_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjwell0u9/f1.bed -b /tmp/tmpjwell0u9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpo43gpxmw/f1.bed -b /tmp/tmpo43gpxmw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpny720nq0/f1.bed -b /tmp/tmpny720nq0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp92rgzwfg/f1.bed -b /tmp/tmp92rgzwfg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpejpr8oqv/f1.bed -b /tmp/tmpejpr8oqv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmph19jamdh/f1.bed -b /tmp/tmph19jamdh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7ddfkbhn/f1.bed -b /tmp/tmp7ddfkbhn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7k977ey6/f1.bed -b /tmp/tmp7k977ey6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1t853ijy/f1.bed -b /tmp/tmp1t853ijy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0d4ks70c/f1.bed -b /tmp/tmp0d4ks70c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0m4jf9sx/f1.bed -b /tmp/tmp0m4jf9sx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_ssk4xqv/f1.bed -b /tmp/tmp_ssk4xqv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6qr8fy_4/f1.bed -b /tmp/tmp6qr8fy_4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp67wseabx/f1.bed -b /tmp/tmp67wseabx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyr9ybi7j/f1.bed -b /tmp/tmpyr9ybi7j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwz3t8a7x/f1.bed -b /tmp/tmpwz3t8a7x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpu9tube05/f1.bed -b /tmp/tmpu9tube05/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm4feqh4c/f1.bed -b /tmp/tmpm4feqh4c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpocqj3rjc/f1.bed -b /tmp/tmpocqj3rjc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpkqy14i7m/f1.bed -b /tmp/tmpkqy14i7m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2u2tzg42/f1.bed -b /tmp/tmp2u2tzg42/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcqoaf3jc/f1.bed -b /tmp/tmpcqoaf3jc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmbyr6kvz/f1.bed -b /tmp/tmpmbyr6kvz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8856827 8858990 a 0 + 1 chr1 4079104 4085831 a 0 - 2 chr1 9402834 9412833 a 0 - 3 chr4 835776 836992 a 0 - 4 chr10 8490560 8498770 a 0 + 5 chr14 5742956 5746096 a 0 + 6 chrM 6895483 6905482 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcknr8ppx/f1.bed -b /tmp/tmpcknr8ppx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpl5hfuizz/f1.bed -b /tmp/tmpl5hfuizz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 7810 a 0 + 1 chr1 1 7810 a 0 - Chromosome Start End Name Score Strand 0 chr1 7835236 7841938 a 0 + 1 chr1 1963273 1964331 a 0 - 2 chr1 3568491 3576520 a 0 - 3 chr1 3403064 3404928 a 0 - 4 chr1 4469010 4476044 a 0 - 5 chr1 8703686 8713646 a 0 - 6 chr13 883978 884093 a 0 - 7 chr15 4624352 4626826 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpi97ceahw/f1.bed -b /tmp/tmpi97ceahw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 7810 a 0 + 1 chr1 1 7810 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp025or6i9/f1.bed -b /tmp/tmp025or6i9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4179292 4189291 a 0 + 1 chr1 9417493 9425277 a 0 - 2 chr16 2753606 2755803 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfjv2v1yy/f1.bed -b /tmp/tmpfjv2v1yy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0bjljxe5/f1.bed -b /tmp/tmp0bjljxe5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9037451 9041987 a 0 + 1 chr1 9037451 9041967 a 0 + 2 chr1 9037451 9046360 a 0 + 3 chr1 9037451 9046588 a 0 + 4 chr1 9037451 9041868 a 0 - 5 chr3 9037451 9046392 a 0 - 6 chr5 9037451 9042928 a 0 - 7 chr13 9037451 9039427 a 0 + 8 chr13 9037451 9045361 a 0 - 9 chr15 9037451 9044853 a 0 + 10 chr18 9037451 9041595 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyrz2_6ih/f1.bed -b /tmp/tmpyrz2_6ih/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6w4n21j1/f1.bed -b /tmp/tmp6w4n21j1/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 3747651 3751087 a 0 + 1 chr1 1 3437 a 0 - 2 chr1 3138239 3141675 a 0 - 3 chr1 1 6443 a 0 - 4 chr2 1 3437 a 0 + 5 chr7 6392841 6401094 a 0 + 6 chr11 1 3483 a 0 - 7 chr15 1 3437 a 0 + 8 chrX 5990408 5993844 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0oyd5jdg/f1.bed -b /tmp/tmp0oyd5jdg/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnp4s6fdk/f1.bed -b /tmp/tmpnp4s6fdk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7339844 7342320 a 0 - 1 chr10 3904166 3913320 a 0 + 2 chr12 7339844 7342294 a 0 + 3 chr15 3968149 3970141 a 0 + 4 chr16 7339844 7348578 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7usapqbv/f1.bed -b /tmp/tmp7usapqbv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2b1wlhyt/f1.bed -b /tmp/tmp2b1wlhyt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1147423 1152447 a 0 + 1 chr1 8275832 8276763 a 0 - 2 chr14 8893399 8894330 a 0 + 3 chr16 8439071 8446118 a 0 - 4 chr17 9953014 9956841 a 0 - 5 chrM 6839800 6842386 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpheudb2jm/f1.bed -b /tmp/tmpheudb2jm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpae50mzeu/f1.bed -b /tmp/tmpae50mzeu/f2.bed Chromosome Start End Name Score Strand 0 chr5 3447824 3447825 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2731 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptvq26yjx/f1.bed -b /tmp/tmptvq26yjx/f2.bed Chromosome Start End Name Score Strand 0 chr5 3447824 3447825 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpklfovyuz/f1.bed -b /tmp/tmpklfovyuz/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9946297 9950922 a 0 + 1 chr1 5158154 5162765 a 0 - 2 chr1 9074221 9078534 a 0 - 3 chr1 8040968 8045963 a 0 - 4 chrX 4412418 4416489 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpb2qeqb54/f1.bed -b /tmp/tmpb2qeqb54/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsqatf6x4/f1.bed -b /tmp/tmpsqatf6x4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 4764953 4767336 a 0 + 2 chr1 5968701 5978700 a 0 + 3 chr1 3126763 3129365 a 0 + 4 chr1 6267313 6275521 a 0 + 5 chr14 7911921 7919914 a 0 - 6 chr18 5256725 5262068 a 0 + 7 chrX 8661472 8670507 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyecf32oi/f1.bed -b /tmp/tmpyecf32oi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpawy4ehvm/f1.bed -b /tmp/tmpawy4ehvm/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8351134 8357780 a 0 + 1 chr1 8351134 8360351 a 0 + 2 chr1 8351134 8357780 a 0 - 3 chr1 8351134 8359056 a 0 - 4 chr1 8351134 8353296 a 0 - 5 chr12 8351134 8354617 a 0 - 6 chr13 10000000 10006646 a 0 + 7 chr17 8351134 8353878 a 0 - 8 chr20 8351134 8360049 a 0 - 9 chr22 8351134 8353820 a 0 - 10 chrX 8351134 8357780 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpuxnlleio/f1.bed -b /tmp/tmpuxnlleio/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpinwcceqi/f1.bed -b /tmp/tmpinwcceqi/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7895140 7903814 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdc9i99j1/f1.bed -b /tmp/tmpdc9i99j1/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpom0zizsx/f1.bed -b /tmp/tmpom0zizsx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5261463 5271079 a 0 + 1 chr1 1 682 a 0 + 2 chr1 6701369 6705153 a 0 - 3 chr1 3291322 3300201 a 0 - 4 chr2 8523351 8530730 a 0 + 5 chr11 6514284 6523163 a 0 + 6 chr12 1977817 1979907 a 0 + 7 chr14 9161596 9162865 a 0 + 8 chr14 2980778 2984402 a 0 + 9 chr17 7084549 7092374 a 0 + 10 chr20 1732706 1735039 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpier_g4vk/f1.bed -b /tmp/tmpier_g4vk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm4ernzcy/f1.bed -b /tmp/tmpm4ernzcy/f2.bed Chromosome Start End Name Score Strand 0 chr1 9547260 9547261 a 0 - Chromosome Start End Name Score Strand 0 chr1 7420740 7420742 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4tjn_5u8/f1.bed -b /tmp/tmp4tjn_5u8/f2.bed Chromosome Start End Name Score Strand 0 chr1 9547260 9547261 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmph4zy0asj/f1.bed -b /tmp/tmph4zy0asj/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9288237 9296573 a 0 + 1 chr1 6688791 6695890 a 0 + 2 chr1 9955591 9964282 a 0 + 3 chr1 9215273 9225115 a 0 + 4 chr1 131923 133554 a 0 - 5 chr1 5795643 5803855 a 0 - 6 chr1 6606005 6611959 a 0 - 7 chr1 4659415 4666710 a 0 - 8 chr1 7861429 7863550 a 0 - 9 chr8 4171613 4177660 a 0 - 10 chr14 9091445 9101019 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdqmudfoo/f1.bed -b /tmp/tmpdqmudfoo/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpoghp7o2q/f1.bed -b /tmp/tmpoghp7o2q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6193 a 0 + 1 chr1 1 6193 a 0 - 2 chr1 1 6193 a 0 - Chromosome Start End Name Score Strand 0 chr1 1455865 1455867 a 0 + 1 chr1 5817397 5817399 a 0 + 2 chr4 1402039 1402041 a 0 + 3 chr5 1248138 1248140 a 0 - 4 chr12 6168885 6168887 a 0 + 5 chr13 7193387 7193389 a 0 + 6 chr19 8951565 8958281 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbexkempa/f1.bed -b /tmp/tmpbexkempa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 6193 a 0 + 1 chr1 1 6193 a 0 - 2 chr1 1 6193 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe21k88bl/f1.bed -b /tmp/tmpe21k88bl/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + 2 chr1 65537 65538 a 0 + 3 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 6564720 6574720 a 0 + 1 chr1 6262037 6268468 a 0 + 2 chr1 9973149 9980627 a 0 - 3 chr1 6346928 6356927 a 0 - 4 chr1 3696227 3703419 a 0 - 5 chr1 3649689 3651497 a 0 - 6 chr1 3749872 3751069 a 0 - 7 chr1 283056 289339 a 0 - 8 chr1 3224915 3227033 a 0 - 9 chr12 4985280 4991784 a 0 - 10 chrM 8005833 8011484 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2u2in0bj/f1.bed -b /tmp/tmp2u2in0bj/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + 2 chr1 65537 65538 a 0 + 3 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfvtlozc_/f1.bed -b /tmp/tmpfvtlozc_/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr15 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 9337842 9347842 a 0 + 1 chr1 2903772 2913000 a 0 + 2 chr1 2253390 2261605 a 0 - 3 chr1 8653702 8663091 a 0 - 4 chr1 8653702 8656366 a 0 - 5 chr1 8653702 8655824 a 0 - 6 chr1 1395144 1397723 a 0 - 7 chr5 9942278 9948302 a 0 - 8 chr14 8653702 8653964 a 0 + 9 chrM 4661333 4663519 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2pbzhuwv/f1.bed -b /tmp/tmp2pbzhuwv/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr15 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpkn7tf_nl/f1.bed -b /tmp/tmpkn7tf_nl/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + 2 chr1 65537 65538 a 0 + 3 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1152452 1159024 a 0 + 1 chr1 9880513 9883200 a 0 + 2 chr1 1152452 1159073 a 0 + 3 chr1 1678765 1680490 a 0 + 4 chr1 1152452 1158785 a 0 + 5 chr1 80888 85430 a 0 - 6 chr4 7294067 7298917 a 0 - 7 chr6 1152452 1157801 a 0 + 8 chr11 2253551 2259320 a 0 + 9 chr14 1152452 1154254 a 0 + 10 chr17 1152452 1160942 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5siq5gpc/f1.bed -b /tmp/tmp5siq5gpc/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + 2 chr1 65537 65538 a 0 + 3 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0pwao8t8/f1.bed -b /tmp/tmp0pwao8t8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 9529 a 0 + 1 chr1 1 9529 a 0 + 2 chr1 1 9529 a 0 + Chromosome Start End Name Score Strand 0 chr1 2945763 2953734 a 0 + 1 chr1 7857211 7857237 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_z4nidjd/f1.bed -b /tmp/tmp_z4nidjd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 9529 a 0 + 1 chr1 1 9529 a 0 + 2 chr1 1 9529 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp92nvhwk9/f1.bed -b /tmp/tmp92nvhwk9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8018674 8025241 a 0 + 1 chr1 5376741 5385471 a 0 + 2 chr1 7175144 7177807 a 0 + 3 chr1 6440453 6440516 a 0 + 4 chr1 6482993 6487484 a 0 + 5 chr1 2489672 2491839 a 0 + 6 chr1 2766403 2771080 a 0 + 7 chr1 1619881 1619934 a 0 + 8 chr13 6397767 6404199 a 0 + 9 chr14 7442743 7447653 a 0 + 10 chr18 5862911 5862912 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9iw7h8tm/f1.bed -b /tmp/tmp9iw7h8tm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7pfy75jj/f1.bed -b /tmp/tmp7pfy75jj/f2.bed Chromosome Start End Name Score Strand 0 chr1 2494027 2494028 a 0 + Chromosome Start End Name Score Strand 0 chr1 36691 37036 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppn22cdju/f1.bed -b /tmp/tmppn22cdju/f2.bed Chromosome Start End Name Score Strand 0 chr1 2494027 2494028 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpml6setua/f1.bed -b /tmp/tmpml6setua/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4600240 4602052 a 0 + 1 chr1 3269890 3275308 a 0 + 2 chr1 10000000 10003543 a 0 + 3 chr1 9175666 9185175 a 0 - 4 chr1 8376770 8383600 a 0 - 5 chr1 2657226 2665584 a 0 - 6 chr3 817727 823898 a 0 + 7 chr4 8993342 8996357 a 0 + 8 chr8 2515747 2518591 a 0 - 9 chr12 995250 997728 a 0 - 10 chrX 937518 939545 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpefdgg6gm/f1.bed -b /tmp/tmpefdgg6gm/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxjedcnpq/f1.bed -b /tmp/tmpxjedcnpq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7420744 7423276 a 0 + 1 chr1 3411905 3416394 a 0 + 2 chr1 2570417 2574906 a 0 + 3 chr1 6775585 6780074 a 0 - 4 chr1 5928645 5933134 a 0 - 5 chr1 84394 88883 a 0 - 6 chr1 1541679 1546168 a 0 - 7 chr3 8940820 8945309 a 0 + 8 chr11 1 4490 a 0 - 9 chr18 279789 284278 a 0 - 10 chrM 7983537 7988026 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpp_i6nud6/f1.bed -b /tmp/tmpp_i6nud6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3gbqhbis/f1.bed -b /tmp/tmp3gbqhbis/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 4852 a 0 + 1 chr1 1 4852 a 0 - Chromosome Start End Name Score Strand 0 chr1 4124327 4128315 a 0 - 1 chr3 9338388 9342376 a 0 - 2 chr4 2396185 2402495 a 0 + 3 chr10 5087270 5091258 a 0 + 4 chr17 7677555 7681543 a 0 + 5 chr20 5249225 5253213 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgcb1ah4g/f1.bed -b /tmp/tmpgcb1ah4g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 4852 a 0 + 1 chr1 1 4852 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpz5zwlzcs/f1.bed -b /tmp/tmpz5zwlzcs/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3473690 3474436 a 0 + 1 chr9 9632970 9637176 a 0 - 2 chr9 6122269 6127996 a 0 - 3 chrY 7888654 7893896 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6yn7qqug/f1.bed -b /tmp/tmp6yn7qqug/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvd4438j9/f1.bed -b /tmp/tmpvd4438j9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5335478 5337079 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp649j1dlk/f1.bed -b /tmp/tmp649j1dlk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfx9a5da1/f1.bed -b /tmp/tmpfx9a5da1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 8675 a 0 + 1 chr1 1 8675 a 0 - Chromosome Start End Name Score Strand 0 chr1 1084902 1084969 a 0 + 1 chr1 1084902 1086048 a 0 - 2 chr1 1084902 1092958 a 0 - 3 chr1 1084902 1094138 a 0 - 4 chr1 1084902 1086990 a 0 - 5 chr1 1084902 1084969 a 0 - 6 chr7 1084902 1094129 a 0 + 7 chr11 1084902 1093511 a 0 - 8 chr17 1084902 1091077 a 0 - 9 chr19 1084902 1084969 a 0 + 10 chrY 1084902 1088550 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpx_5eeqm3/f1.bed -b /tmp/tmpx_5eeqm3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 8675 a 0 + 1 chr1 1 8675 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpva1xqvim/f1.bed -b /tmp/tmpva1xqvim/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2756 a 0 + 1 chr1 1 2756 a 0 + 2 chr1 1 2756 a 0 - Chromosome Start End Name Score Strand 0 chr1 5035740 5036971 a 0 + 1 chr1 4644379 4650352 a 0 - 2 chr1 7656715 7656716 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvo_57737/f1.bed -b /tmp/tmpvo_57737/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2756 a 0 + 1 chr1 1 2756 a 0 + 2 chr1 1 2756 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpeh26n2if/f1.bed -b /tmp/tmpeh26n2if/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7701569 7711569 a 0 - 1 chr4 1309687 1318645 a 0 - 2 chr15 9164883 9174779 a 0 - 3 chrY 4165636 4167880 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpak1a9d6s/f1.bed -b /tmp/tmpak1a9d6s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq8edzkuq/f1.bed -b /tmp/tmpq8edzkuq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5954604 5957468 a 0 - 1 chr1 5954604 5957468 a 0 - 2 chr1 5954604 5957468 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8rp6zr5v/f1.bed -b /tmp/tmp8rp6zr5v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpy36fchmh/f1.bed -b /tmp/tmpy36fchmh/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr6 1069456 1070955 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0gwlhk62/f1.bed -b /tmp/tmp0gwlhk62/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpl6le_576/f1.bed -b /tmp/tmpl6le_576/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8967308 8970040 a 0 + 1 chr1 1354496 1363851 a 0 - 2 chr1 44373 48755 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpikfhgscs/f1.bed -b /tmp/tmpikfhgscs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps04_weia/f1.bed -b /tmp/tmps04_weia/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 9963248 9970638 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9yyowj5y/f1.bed -b /tmp/tmp9yyowj5y/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsyyy37q0/f1.bed -b /tmp/tmpsyyy37q0/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 7569490 7578484 a 0 + 1 chr12 2432019 2432020 a 0 + 2 chrM 9669435 9678284 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps_a_1692/f1.bed -b /tmp/tmps_a_1692/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_1py7694/f1.bed -b /tmp/tmp_1py7694/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9005923 9011682 a 0 + 1 chr1 8438034 8446010 a 0 + 2 chr1 6953001 6961340 a 0 + 3 chr1 8950008 8950630 a 0 + 4 chr1 2030840 2038183 a 0 - 5 chr1 9999999 10008210 a 0 - 6 chr1 9349706 9356844 a 0 - 7 chr2 9602218 9606773 a 0 - 8 chr5 3495700 3502542 a 0 - 9 chr12 9617136 9618590 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjshjw9wy/f1.bed -b /tmp/tmpjshjw9wy/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9a4egy5t/f1.bed -b /tmp/tmp9a4egy5t/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr2 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 8065698 8065976 a 0 + 1 chr1 2942968 2948760 a 0 - 2 chr8 8065698 8068880 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpg7w6wi5h/f1.bed -b /tmp/tmpg7w6wi5h/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr2 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_9w70egx/f1.bed -b /tmp/tmp_9w70egx/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + 2 chr1 65537 65538 a 0 + 3 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 6260662 6263205 a 0 + 1 chr1 6260662 6269447 a 0 - 2 chr8 6260662 6269447 a 0 + 3 chr10 6260662 6262935 a 0 + 4 chr12 8295782 8299601 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgwim712e/f1.bed -b /tmp/tmpgwim712e/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + 2 chr1 65537 65538 a 0 + 3 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpck87cnt2/f1.bed -b /tmp/tmpck87cnt2/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4955595 4956389 a 0 - 1 chr1 6427366 6433557 a 0 - 2 chr1 6394350 6400952 a 0 - 3 chr1 9537583 9546931 a 0 - 4 chr1 497073 501480 a 0 - 5 chr1 5932576 5937797 a 0 - 6 chr9 8968054 8972461 a 0 + 7 chr18 1119991 1128568 a 0 - 8 chrM 6486790 6491306 a 0 - 9 chrM 1904934 1912872 a 0 - 10 chrY 2623404 2627811 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp15zpengv/f1.bed -b /tmp/tmp15zpengv/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpk35mrciu/f1.bed -b /tmp/tmpk35mrciu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9959073 9960583 a 0 + 1 chr1 9198109 9203164 a 0 + 2 chr1 9959073 9964128 a 0 + 3 chr12 9959073 9964128 a 0 - 4 chr21 2195739 2200794 a 0 - 5 chrM 8468023 8470499 a 0 + 6 chrM 6526392 6531869 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe7sblqe8/f1.bed -b /tmp/tmpe7sblqe8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqljyhds9/f1.bed -b /tmp/tmpqljyhds9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7459165 7465794 a 0 - 1 chr1 776453 785104 a 0 - 2 chr22 802706 806450 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjtut3m74/f1.bed -b /tmp/tmpjtut3m74/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphhchg1nw/f1.bed -b /tmp/tmphhchg1nw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3912939 3914063 a 0 + 1 chr1 3225516 3234995 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9u7kphi_/f1.bed -b /tmp/tmp9u7kphi_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpow051ykk/f1.bed -b /tmp/tmpow051ykk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7220484 7224186 a 0 + 1 chr1 693646 695922 a 0 + 2 chr1 3769550 3773856 a 0 + 3 chr1 9191332 9199413 a 0 + 4 chr1 2062700 2063852 a 0 - 5 chr1 7140586 7150332 a 0 - 6 chr4 9304171 9304409 a 0 - 7 chr4 9117417 9124838 a 0 - 8 chr13 9193162 9202556 a 0 - 9 chr17 3367649 3369081 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzm4axln7/f1.bed -b /tmp/tmpzm4axln7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8sog2i1b/f1.bed -b /tmp/tmp8sog2i1b/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 7324701 7331147 a 0 + 1 chr1 2142557 2152110 a 0 + 2 chr1 2142557 2145626 a 0 + 3 chr1 2142557 2148060 a 0 - 4 chr1 8583016 8584455 a 0 - 5 chr1 1283411 1291878 a 0 - 6 chr5 2951751 2960797 a 0 + 7 chr6 8542621 8543663 a 0 - 8 chr15 2142557 2151567 a 0 - 9 chr19 417225 418542 a 0 + 10 chr22 2142557 2143510 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfdbo3hhl/f1.bed -b /tmp/tmpfdbo3hhl/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppjd6rwsw/f1.bed -b /tmp/tmppjd6rwsw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 1396 a 0 + 1 chr1 1 1396 a 0 + 2 chr1 1 1396 a 0 + Chromosome Start End Name Score Strand 0 chr10 5979352 5979722 a 0 + 1 chr17 3452980 3454144 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxcj1w_te/f1.bed -b /tmp/tmpxcj1w_te/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6iir8e5g/f1.bed -b /tmp/tmp6iir8e5g/f2.bed ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain55-method_chain55] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ___________ test_three_in_a_row[strandedness_chain22-method_chain22] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 9158838 | 9161912 | a | 0 | + | | | chr2 | 72981 | 81991 | a | 0 | + | | | chrM | 2469487 | 2478497 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 65543 | 66057 | a | 0 | + | | | chr2 | 621598 | 622112 | a | 0 | + | | | chr2 | 8388630 | 8389144 | a | 0 | - | | | chr2 | 133378 | 133892 | a | 0 | - | | | chr2 | 8520705 | 8521219 | a | 0 | - | | | chr2 | 10000000 | 10000514 | a | 0 | - | | | chr2 | 4778486 | 4779000 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 65543 | 66057 | a | 0 | + | | | chr2 | 621598 | 622112 | a | 0 | + | | | chr2 | 8388630 | 8389144 | a | 0 | - | | | chr2 | 133378 | 133892 | a | 0 | - | | | chr2 | 8520705 | 8521219 | a | 0 | - | | | chr2 | 10000000 | 10000514 | a | 0 | - | | | chr2 | 4778486 | 4779000 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY+R2/mbHKs3uFsxYKjnzIwMnA4MEJwMTEPIyMDAwMjOEvvr7VHVdHiujfveBrQwcjLIi/IyMPIxcjKyMDBaWC/S11JOVDfkZQYpjTUxymSsZGbmZy0BGsoGMZCxkEGNmZmZkZGHkZWRkAikDEowMbEzsDMrszMxMnIwSbLYeL79ys9bOmFZvzpTWwCAKVNzEwqDDJsDIyFkjC9SjzW8twsTICTSGnZGBGWQIXS0DAD9GJvY=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 135 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________________ test_subtraction[same] ____________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpux9pvnkv/f1.bed -b /tmp/tmpux9pvnkv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnfefxd4v/f1.bed -b /tmp/tmpnfefxd4v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp95os1rg8/f1.bed -b /tmp/tmp95os1rg8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyqz4roeo/f1.bed -b /tmp/tmpyqz4roeo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpiuxcgdgf/f1.bed -b /tmp/tmpiuxcgdgf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo9tvn58s/f1.bed -b /tmp/tmpo9tvn58s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8praof6d/f1.bed -b /tmp/tmp8praof6d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpu1l958b8/f1.bed -b /tmp/tmpu1l958b8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4321xkju/f1.bed -b /tmp/tmp4321xkju/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpb2qta27w/f1.bed -b /tmp/tmpb2qta27w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0a81_qct/f1.bed -b /tmp/tmp0a81_qct/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_lcny931/f1.bed -b /tmp/tmp_lcny931/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxgtp0gzk/f1.bed -b /tmp/tmpxgtp0gzk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_3tuhppn/f1.bed -b /tmp/tmp_3tuhppn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptfpoey0d/f1.bed -b /tmp/tmptfpoey0d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2pjql2n1/f1.bed -b /tmp/tmp2pjql2n1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmnow5g3q/f1.bed -b /tmp/tmpmnow5g3q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3nysk430/f1.bed -b /tmp/tmp3nysk430/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt6dzz_ux/f1.bed -b /tmp/tmpt6dzz_ux/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpf137fltq/f1.bed -b /tmp/tmpf137fltq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjg6lu6sc/f1.bed -b /tmp/tmpjg6lu6sc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4nl_zg4x/f1.bed -b /tmp/tmp4nl_zg4x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptuq6eqdv/f1.bed -b /tmp/tmptuq6eqdv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpb2s_ua7s/f1.bed -b /tmp/tmpb2s_ua7s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeog5jirc/f1.bed -b /tmp/tmpeog5jirc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1hg0y1j_/f1.bed -b /tmp/tmp1hg0y1j_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmgjgfawg/f1.bed -b /tmp/tmpmgjgfawg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx7mj3q0d/f1.bed -b /tmp/tmpx7mj3q0d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprsa988vc/f1.bed -b /tmp/tmprsa988vc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd2yy3941/f1.bed -b /tmp/tmpd2yy3941/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2gucx5bb/f1.bed -b /tmp/tmp2gucx5bb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmps2yj18pq/f1.bed -b /tmp/tmps2yj18pq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkvrdg7by/f1.bed -b /tmp/tmpkvrdg7by/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxc3vhuan/f1.bed -b /tmp/tmpxc3vhuan/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8fhpn506/f1.bed -b /tmp/tmp8fhpn506/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpujw7csdf/f1.bed -b /tmp/tmpujw7csdf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc37_ht23/f1.bed -b /tmp/tmpc37_ht23/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8928k93r/f1.bed -b /tmp/tmp8928k93r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcfvvrazg/f1.bed -b /tmp/tmpcfvvrazg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpaudphkzy/f1.bed -b /tmp/tmpaudphkzy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprl33wsa6/f1.bed -b /tmp/tmprl33wsa6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptra2w1gh/f1.bed -b /tmp/tmptra2w1gh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphoxq77h1/f1.bed -b /tmp/tmphoxq77h1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpm8talj9y/f1.bed -b /tmp/tmpm8talj9y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzepbuxe2/f1.bed -b /tmp/tmpzepbuxe2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7s5x9tm3/f1.bed -b /tmp/tmp7s5x9tm3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpf8tbdr29/f1.bed -b /tmp/tmpf8tbdr29/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt0l78xwp/f1.bed -b /tmp/tmpt0l78xwp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8bh_7l2c/f1.bed -b /tmp/tmp8bh_7l2c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpseok43ku/f1.bed -b /tmp/tmpseok43ku/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbciqqv14/f1.bed -b /tmp/tmpbciqqv14/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpujzd1tif/f1.bed -b /tmp/tmpujzd1tif/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpuyjzu3xd/f1.bed -b /tmp/tmpuyjzu3xd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0b9mscdj/f1.bed -b /tmp/tmp0b9mscdj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdwsicy0d/f1.bed -b /tmp/tmpdwsicy0d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_y_ifv4k/f1.bed -b /tmp/tmp_y_ifv4k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz7_85twk/f1.bed -b /tmp/tmpz7_85twk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzov8d0ea/f1.bed -b /tmp/tmpzov8d0ea/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk1fiv3d2/f1.bed -b /tmp/tmpk1fiv3d2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8h_oqhl_/f1.bed -b /tmp/tmp8h_oqhl_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpasg0menm/f1.bed -b /tmp/tmpasg0menm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnj13clld/f1.bed -b /tmp/tmpnj13clld/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcua_072i/f1.bed -b /tmp/tmpcua_072i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdb1y8k1j/f1.bed -b /tmp/tmpdb1y8k1j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqwfta4pe/f1.bed -b /tmp/tmpqwfta4pe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0zl5i_sz/f1.bed -b /tmp/tmp0zl5i_sz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1i_monin/f1.bed -b /tmp/tmp1i_monin/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmvsm_r1u/f1.bed -b /tmp/tmpmvsm_r1u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj5xd_xi9/f1.bed -b /tmp/tmpj5xd_xi9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnk2zd5q5/f1.bed -b /tmp/tmpnk2zd5q5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprqdmohfz/f1.bed -b /tmp/tmprqdmohfz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1xtowoud/f1.bed -b /tmp/tmp1xtowoud/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3ayqy6gp/f1.bed -b /tmp/tmp3ayqy6gp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpm70y7v46/f1.bed -b /tmp/tmpm70y7v46/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvkpht6jh/f1.bed -b /tmp/tmpvkpht6jh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyw1a6ru0/f1.bed -b /tmp/tmpyw1a6ru0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5o9lvupb/f1.bed -b /tmp/tmp5o9lvupb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3_yzb5jk/f1.bed -b /tmp/tmp3_yzb5jk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbbcpoafw/f1.bed -b /tmp/tmpbbcpoafw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpckco1ati/f1.bed -b /tmp/tmpckco1ati/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp23k5uv85/f1.bed -b /tmp/tmp23k5uv85/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpja_746mp/f1.bed -b /tmp/tmpja_746mp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj1utgyft/f1.bed -b /tmp/tmpj1utgyft/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplt95qxe6/f1.bed -b /tmp/tmplt95qxe6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprmum1tv2/f1.bed -b /tmp/tmprmum1tv2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp0eq0kmo/f1.bed -b /tmp/tmpp0eq0kmo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphkg1acdq/f1.bed -b /tmp/tmphkg1acdq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpar7nv7ez/f1.bed -b /tmp/tmpar7nv7ez/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpavliv5ov/f1.bed -b /tmp/tmpavliv5ov/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprjsbrujw/f1.bed -b /tmp/tmprjsbrujw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc6ljnl7q/f1.bed -b /tmp/tmpc6ljnl7q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp36xknczl/f1.bed -b /tmp/tmp36xknczl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwj2ftly9/f1.bed -b /tmp/tmpwj2ftly9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp7207oho/f1.bed -b /tmp/tmpp7207oho/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1td0yn79/f1.bed -b /tmp/tmp1td0yn79/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9ny85g46/f1.bed -b /tmp/tmp9ny85g46/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt6ypoa99/f1.bed -b /tmp/tmpt6ypoa99/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2l8zl2z4/f1.bed -b /tmp/tmp2l8zl2z4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbou130pk/f1.bed -b /tmp/tmpbou130pk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph4bszc_h/f1.bed -b /tmp/tmph4bszc_h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphczrivm9/f1.bed -b /tmp/tmphczrivm9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_0qpbccy/f1.bed -b /tmp/tmp_0qpbccy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5922dc1d/f1.bed -b /tmp/tmp5922dc1d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc7h8snp_/f1.bed -b /tmp/tmpc7h8snp_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd6p370kv/f1.bed -b /tmp/tmpd6p370kv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwo7odh9r/f1.bed -b /tmp/tmpwo7odh9r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe0dy_sax/f1.bed -b /tmp/tmpe0dy_sax/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpf5c3kn2v/f1.bed -b /tmp/tmpf5c3kn2v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpixear015/f1.bed -b /tmp/tmpixear015/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp78vxzdq3/f1.bed -b /tmp/tmp78vxzdq3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4v6qo6bj/f1.bed -b /tmp/tmp4v6qo6bj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg795x1p6/f1.bed -b /tmp/tmpg795x1p6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3t7py2bx/f1.bed -b /tmp/tmp3t7py2bx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe4pic2p3/f1.bed -b /tmp/tmpe4pic2p3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph8xabmfy/f1.bed -b /tmp/tmph8xabmfy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt9kc4_cd/f1.bed -b /tmp/tmpt9kc4_cd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5k415zj6/f1.bed -b /tmp/tmp5k415zj6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbswdftwd/f1.bed -b /tmp/tmpbswdftwd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpma__f0z0/f1.bed -b /tmp/tmpma__f0z0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpauu3ysz1/f1.bed -b /tmp/tmpauu3ysz1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp85_cny8q/f1.bed -b /tmp/tmp85_cny8q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjlohcjpi/f1.bed -b /tmp/tmpjlohcjpi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp41eoflgg/f1.bed -b /tmp/tmp41eoflgg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8asw8uqa/f1.bed -b /tmp/tmp8asw8uqa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp14a2go5r/f1.bed -b /tmp/tmp14a2go5r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgen_lr5a/f1.bed -b /tmp/tmpgen_lr5a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8tk1hodj/f1.bed -b /tmp/tmp8tk1hodj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6b7e6p_f/f1.bed -b /tmp/tmp6b7e6p_f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk33oezhc/f1.bed -b /tmp/tmpk33oezhc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvovwoh07/f1.bed -b /tmp/tmpvovwoh07/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp16q3lq7s/f1.bed -b /tmp/tmp16q3lq7s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4xnwnnqn/f1.bed -b /tmp/tmp4xnwnnqn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1jalx0um/f1.bed -b /tmp/tmp1jalx0um/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpupn0jqez/f1.bed -b /tmp/tmpupn0jqez/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpi_mi_bj8/f1.bed -b /tmp/tmpi_mi_bj8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[upstream-False-False-last] ___________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5377281 | 5378050 | a | 0 | - | | | chr1 | 5377281 | 5377282 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAFx5nofGGBVBmN7dQoAAAEAUlINAAsAXQMAAAMAAAABAWZ6HxgABQABAABVAAAAAA4AAQAB') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdzmeux6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzmeux6k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgsc6yibw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgsc6yibw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf673cy04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf673cy04/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp20a947hj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20a947hj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfgvki1u2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgvki1u2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoe1imojm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoe1imojm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprg1l_b7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprg1l_b7r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkt3u91pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkt3u91pf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbuj6kui9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbuj6kui9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpktgvvqk0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktgvvqk0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmilx9zb3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmilx9zb3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgcaqlza8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgcaqlza8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqdhqx37a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdhqx37a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8i0ys3kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8i0ys3kr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8g_qum5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8g_qum5j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppavm4kml/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppavm4kml/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsirckus6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsirckus6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoh70rtpw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoh70rtpw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprn4eieht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprn4eieht/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphjvj6bpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjvj6bpk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_en0ww1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_en0ww1l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0n_wjktt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0n_wjktt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplhp3etpy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplhp3etpy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7r9q0u6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7r9q0u6g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppey1nc8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppey1nc8d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpebvg2wm1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebvg2wm1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6unm2r5z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6unm2r5z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6wx3yi82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wx3yi82/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplvmvd3wn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvmvd3wn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkc76n0nk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkc76n0nk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp14st9r65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp14st9r65/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqy8sr_ph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqy8sr_ph/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1x9pwqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1x9pwqu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr83rteut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr83rteut/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqx3h6xjq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqx3h6xjq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjlbyuqfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjlbyuqfh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptl8e8gu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptl8e8gu9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqb02jf83/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqb02jf83/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ojm6aog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ojm6aog/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp077j4pr7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp077j4pr7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx6ssx9yy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6ssx9yy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvo6cgpc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvo6cgpc6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu_xc0mr1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_xc0mr1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ccpmczt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ccpmczt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzopdy1e0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzopdy1e0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4c2l25bs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4c2l25bs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr3r2xcrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3r2xcrz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplaofvk91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplaofvk91/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp64s5zen7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64s5zen7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4wjf29vl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4wjf29vl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpew2ii1w8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpew2ii1w8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzvmj8lqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvmj8lqh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2f3m4lfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f3m4lfu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp74k4mk4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74k4mk4o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptozemfdh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptozemfdh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppjx2qysd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjx2qysd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqvdq3i9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqvdq3i9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpguoyjxdi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpguoyjxdi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiju6rrmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiju6rrmi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnfn_6xb5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfn_6xb5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2qvxd78l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qvxd78l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_tpi7z9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_tpi7z9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps4x_r1he/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps4x_r1he/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp66mms393/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66mms393/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw8mbklc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw8mbklc7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy6dompa9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6dompa9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7_rnxj59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_rnxj59/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp44un5_vn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44un5_vn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpslvtn9yb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpslvtn9yb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiw4fnduz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiw4fnduz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvy4p4nlp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvy4p4nlp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_wpjxuhc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_wpjxuhc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprutu9zxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprutu9zxj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr_4jfp96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr_4jfp96/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp32scrgna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32scrgna/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwsnf7i81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsnf7i81/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpibm5gi5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibm5gi5w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6vri34ia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6vri34ia/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpny8p9kiq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpny8p9kiq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz6jmezcd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz6jmezcd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw9urvvwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw9urvvwx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpip0ubw8q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpip0ubw8q/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain56-method_chain56] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 113 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain23-method_chain23] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1048835 | 1049092 | a | 0 | + | E | chr1 | 1048835 | 1049092 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9374723 | 9375237 | a | 0 | + | E | chr2 | 9374723 | 9375237 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2NhZGRkjmRnYGQAIkYBRiYGRiCTgZ3Jl43hCVv2snue4lL/GJjBsgz5/TxMDCxMIAVAbWCaAQDSDwZU') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________________ test_subtraction[opposite] __________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppi1xq7pj/f1.bed -b /tmp/tmppi1xq7pj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2e89rf93/f1.bed -b /tmp/tmp2e89rf93/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpn1i97r2h/f1.bed -b /tmp/tmpn1i97r2h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpl49a01m7/f1.bed -b /tmp/tmpl49a01m7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0ji464tl/f1.bed -b /tmp/tmp0ji464tl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr786qu1p/f1.bed -b /tmp/tmpr786qu1p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplnkg1qhc/f1.bed -b /tmp/tmplnkg1qhc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwh5b64yo/f1.bed -b /tmp/tmpwh5b64yo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4nent94q/f1.bed -b /tmp/tmp4nent94q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_j5z90qo/f1.bed -b /tmp/tmp_j5z90qo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpro842c41/f1.bed -b /tmp/tmpro842c41/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0f3l_m4c/f1.bed -b /tmp/tmp0f3l_m4c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0whddt5r/f1.bed -b /tmp/tmp0whddt5r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8n4slosx/f1.bed -b /tmp/tmp8n4slosx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzn1zg2ul/f1.bed -b /tmp/tmpzn1zg2ul/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf5teocwz/f1.bed -b /tmp/tmpf5teocwz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp19n8dg1p/f1.bed -b /tmp/tmp19n8dg1p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz3yd30ml/f1.bed -b /tmp/tmpz3yd30ml/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpng224zoz/f1.bed -b /tmp/tmpng224zoz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptfwffe57/f1.bed -b /tmp/tmptfwffe57/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwppll218/f1.bed -b /tmp/tmpwppll218/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxip1zbit/f1.bed -b /tmp/tmpxip1zbit/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpecmwdw3x/f1.bed -b /tmp/tmpecmwdw3x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqhvfxj9_/f1.bed -b /tmp/tmpqhvfxj9_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5hn7rzda/f1.bed -b /tmp/tmp5hn7rzda/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps3lxnhct/f1.bed -b /tmp/tmps3lxnhct/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprnsu05c7/f1.bed -b /tmp/tmprnsu05c7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1vih8r55/f1.bed -b /tmp/tmp1vih8r55/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6h22a5fp/f1.bed -b /tmp/tmp6h22a5fp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa5jk0gnm/f1.bed -b /tmp/tmpa5jk0gnm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjuay671z/f1.bed -b /tmp/tmpjuay671z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpon19j58m/f1.bed -b /tmp/tmpon19j58m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3wxubm80/f1.bed -b /tmp/tmp3wxubm80/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpb41q9gc4/f1.bed -b /tmp/tmpb41q9gc4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpptkqabsj/f1.bed -b /tmp/tmpptkqabsj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpieej1_gt/f1.bed -b /tmp/tmpieej1_gt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptt2vsxsc/f1.bed -b /tmp/tmptt2vsxsc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdxp24scd/f1.bed -b /tmp/tmpdxp24scd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7jn36uj4/f1.bed -b /tmp/tmp7jn36uj4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5fiacfbr/f1.bed -b /tmp/tmp5fiacfbr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpepmtt59e/f1.bed -b /tmp/tmpepmtt59e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp69dcg15y/f1.bed -b /tmp/tmp69dcg15y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5kuc9bul/f1.bed -b /tmp/tmp5kuc9bul/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp_2kxwh1/f1.bed -b /tmp/tmpp_2kxwh1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3wybxodm/f1.bed -b /tmp/tmp3wybxodm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgtnbd9dy/f1.bed -b /tmp/tmpgtnbd9dy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2lxygz93/f1.bed -b /tmp/tmp2lxygz93/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbb7tc7i8/f1.bed -b /tmp/tmpbb7tc7i8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgs1m95mg/f1.bed -b /tmp/tmpgs1m95mg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpch9sud9c/f1.bed -b /tmp/tmpch9sud9c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgtfbna4v/f1.bed -b /tmp/tmpgtfbna4v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiaz54jdu/f1.bed -b /tmp/tmpiaz54jdu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpk7qawfxl/f1.bed -b /tmp/tmpk7qawfxl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptfvpud2h/f1.bed -b /tmp/tmptfvpud2h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpayjfgy86/f1.bed -b /tmp/tmpayjfgy86/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr1v1cv86/f1.bed -b /tmp/tmpr1v1cv86/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsp4dr9v_/f1.bed -b /tmp/tmpsp4dr9v_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkqot0v4i/f1.bed -b /tmp/tmpkqot0v4i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7dfsu8u4/f1.bed -b /tmp/tmp7dfsu8u4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw25who10/f1.bed -b /tmp/tmpw25who10/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1hnw0d__/f1.bed -b /tmp/tmp1hnw0d__/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx1s5cnlh/f1.bed -b /tmp/tmpx1s5cnlh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpslhcd573/f1.bed -b /tmp/tmpslhcd573/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkin185tz/f1.bed -b /tmp/tmpkin185tz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp60jd4drl/f1.bed -b /tmp/tmp60jd4drl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpq7x5p637/f1.bed -b /tmp/tmpq7x5p637/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr7y6x21p/f1.bed -b /tmp/tmpr7y6x21p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm_dvu2f3/f1.bed -b /tmp/tmpm_dvu2f3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp20astp5g/f1.bed -b /tmp/tmp20astp5g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkp1_jahz/f1.bed -b /tmp/tmpkp1_jahz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgtfoc264/f1.bed -b /tmp/tmpgtfoc264/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpstavpu4b/f1.bed -b /tmp/tmpstavpu4b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5z3a20tl/f1.bed -b /tmp/tmp5z3a20tl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp55lni76/f1.bed -b /tmp/tmpp55lni76/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpipqbh2hu/f1.bed -b /tmp/tmpipqbh2hu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmwwwtumu/f1.bed -b /tmp/tmpmwwwtumu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzfx0wgd7/f1.bed -b /tmp/tmpzfx0wgd7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp55qb6h85/f1.bed -b /tmp/tmp55qb6h85/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzf8xk3t9/f1.bed -b /tmp/tmpzf8xk3t9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt3rsffn5/f1.bed -b /tmp/tmpt3rsffn5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3inhm3i1/f1.bed -b /tmp/tmp3inhm3i1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdfz5i48d/f1.bed -b /tmp/tmpdfz5i48d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprrfy7s5v/f1.bed -b /tmp/tmprrfy7s5v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw7k180c7/f1.bed -b /tmp/tmpw7k180c7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg246sekm/f1.bed -b /tmp/tmpg246sekm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbvph9bms/f1.bed -b /tmp/tmpbvph9bms/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpq_8hv4eh/f1.bed -b /tmp/tmpq_8hv4eh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp835z823v/f1.bed -b /tmp/tmp835z823v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpby7in549/f1.bed -b /tmp/tmpby7in549/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg3iof49y/f1.bed -b /tmp/tmpg3iof49y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpo6kljueo/f1.bed -b /tmp/tmpo6kljueo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8zq2qs92/f1.bed -b /tmp/tmp8zq2qs92/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdrg31x15/f1.bed -b /tmp/tmpdrg31x15/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfwe0iss_/f1.bed -b /tmp/tmpfwe0iss_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8bso1w1m/f1.bed -b /tmp/tmp8bso1w1m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcg16yiee/f1.bed -b /tmp/tmpcg16yiee/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfsa5a6hc/f1.bed -b /tmp/tmpfsa5a6hc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuux2f6m_/f1.bed -b /tmp/tmpuux2f6m_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4maxmr_k/f1.bed -b /tmp/tmp4maxmr_k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt_5pknkq/f1.bed -b /tmp/tmpt_5pknkq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8tjal3yp/f1.bed -b /tmp/tmp8tjal3yp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjgr1lywc/f1.bed -b /tmp/tmpjgr1lywc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpirdczhzy/f1.bed -b /tmp/tmpirdczhzy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3jlmkvjq/f1.bed -b /tmp/tmp3jlmkvjq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxwo4yqx5/f1.bed -b /tmp/tmpxwo4yqx5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpop0ey06q/f1.bed -b /tmp/tmpop0ey06q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp299ds66e/f1.bed -b /tmp/tmp299ds66e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppvpfr0cv/f1.bed -b /tmp/tmppvpfr0cv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_eys_mti/f1.bed -b /tmp/tmp_eys_mti/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9k7ty4x0/f1.bed -b /tmp/tmp9k7ty4x0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc8k1x8i8/f1.bed -b /tmp/tmpc8k1x8i8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa8fnhgnq/f1.bed -b /tmp/tmpa8fnhgnq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsl1jbsst/f1.bed -b /tmp/tmpsl1jbsst/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps5vr6rfh/f1.bed -b /tmp/tmps5vr6rfh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0918uwja/f1.bed -b /tmp/tmp0918uwja/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz1t4bx04/f1.bed -b /tmp/tmpz1t4bx04/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm522en5u/f1.bed -b /tmp/tmpm522en5u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphtavwln8/f1.bed -b /tmp/tmphtavwln8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpic_02bs1/f1.bed -b /tmp/tmpic_02bs1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqnz0k5ww/f1.bed -b /tmp/tmpqnz0k5ww/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf7uhwq5y/f1.bed -b /tmp/tmpf7uhwq5y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp98aqrtj0/f1.bed -b /tmp/tmp98aqrtj0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiugbsadu/f1.bed -b /tmp/tmpiugbsadu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3fcxozcl/f1.bed -b /tmp/tmp3fcxozcl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwhn1hrk_/f1.bed -b /tmp/tmpwhn1hrk_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmogm9h80/f1.bed -b /tmp/tmpmogm9h80/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbsax2_lc/f1.bed -b /tmp/tmpbsax2_lc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpck67bxcx/f1.bed -b /tmp/tmpck67bxcx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpimlbj1s0/f1.bed -b /tmp/tmpimlbj1s0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8zlqz320/f1.bed -b /tmp/tmp8zlqz320/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqs0iwxf9/f1.bed -b /tmp/tmpqs0iwxf9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa7xs5jhd/f1.bed -b /tmp/tmpa7xs5jhd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppet_c0i0/f1.bed -b /tmp/tmppet_c0i0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfryo1tve/f1.bed -b /tmp/tmpfryo1tve/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3bvebz7a/f1.bed -b /tmp/tmp3bvebz7a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm91ffi9z/f1.bed -b /tmp/tmpm91ffi9z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_lcy2jh0/f1.bed -b /tmp/tmp_lcy2jh0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpthuji7ut/f1.bed -b /tmp/tmpthuji7ut/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgz420qp0/f1.bed -b /tmp/tmpgz420qp0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkr6ieveo/f1.bed -b /tmp/tmpkr6ieveo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9rogoa8r/f1.bed -b /tmp/tmp9rogoa8r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp95jwh5m5/f1.bed -b /tmp/tmp95jwh5m5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgdek287e/f1.bed -b /tmp/tmpgdek287e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppdb3oacf/f1.bed -b /tmp/tmppdb3oacf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxc89vtcx/f1.bed -b /tmp/tmpxc89vtcx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuxpqvfbi/f1.bed -b /tmp/tmpuxpqvfbi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7j3hdk6b/f1.bed -b /tmp/tmp7j3hdk6b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf_9877ro/f1.bed -b /tmp/tmpf_9877ro/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpy8djzm8p/f1.bed -b /tmp/tmpy8djzm8p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpy_qx0qq1/f1.bed -b /tmp/tmpy_qx0qq1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp223kmoz7/f1.bed -b /tmp/tmp223kmoz7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpalt7amud/f1.bed -b /tmp/tmpalt7amud/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcmtz9okn/f1.bed -b /tmp/tmpcmtz9okn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4t5yhyps/f1.bed -b /tmp/tmp4t5yhyps/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc8nxw12f/f1.bed -b /tmp/tmpc8nxw12f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7hcj3a1t/f1.bed -b /tmp/tmp7hcj3a1t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp40p9pzqq/f1.bed -b /tmp/tmp40p9pzqq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5rw1397f/f1.bed -b /tmp/tmp5rw1397f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpka9dbwj1/f1.bed -b /tmp/tmpka9dbwj1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1im6zfbp/f1.bed -b /tmp/tmp1im6zfbp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_0c4ckdr/f1.bed -b /tmp/tmp_0c4ckdr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg69y4ujy/f1.bed -b /tmp/tmpg69y4ujy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpn4k9wvgc/f1.bed -b /tmp/tmpn4k9wvgc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmvrgmp9t/f1.bed -b /tmp/tmpmvrgmp9t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpy9najml_/f1.bed -b /tmp/tmpy9najml_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8wwkipz6/f1.bed -b /tmp/tmp8wwkipz6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxwj1ixzi/f1.bed -b /tmp/tmpxwj1ixzi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8hl3knem/f1.bed -b /tmp/tmp8hl3knem/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7egqyanc/f1.bed -b /tmp/tmp7egqyanc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0i2bs1ex/f1.bed -b /tmp/tmp0i2bs1ex/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxzw5_63d/f1.bed -b /tmp/tmpxzw5_63d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpstc14a03/f1.bed -b /tmp/tmpstc14a03/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpft5k5sp4/f1.bed -b /tmp/tmpft5k5sp4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9xt2ka44/f1.bed -b /tmp/tmp9xt2ka44/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuuz99qcd/f1.bed -b /tmp/tmpuuz99qcd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1eqpkz_a/f1.bed -b /tmp/tmp1eqpkz_a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1_tc8dkm/f1.bed -b /tmp/tmp1_tc8dkm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5sumjz8n/f1.bed -b /tmp/tmp5sumjz8n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsrmw43q5/f1.bed -b /tmp/tmpsrmw43q5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps8obs4di/f1.bed -b /tmp/tmps8obs4di/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsdq67mkt/f1.bed -b /tmp/tmpsdq67mkt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr5k1vx36/f1.bed -b /tmp/tmpr5k1vx36/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi0ds7wo9/f1.bed -b /tmp/tmpi0ds7wo9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6crrwc9q/f1.bed -b /tmp/tmp6crrwc9q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9_fwfbbz/f1.bed -b /tmp/tmp9_fwfbbz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpq3p1ucog/f1.bed -b /tmp/tmpq3p1ucog/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________ test_k_nearest[upstream-True-opposite-last] __________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGOGBkxBBiAAAAngAG') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_0krewly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_0krewly/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphj2yb2xy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphj2yb2xy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjapa1pfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjapa1pfu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphbye1qv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbye1qv5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4cyyiyy6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cyyiyy6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp75p1p1xz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75p1p1xz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph6dlne6s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6dlne6s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpai352v_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpai352v_l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp14dix370/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp14dix370/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqflx2lwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqflx2lwh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmumbmh_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmumbmh_c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsay8c1yr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsay8c1yr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5er5z2ef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5er5z2ef/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuh8pf7zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuh8pf7zc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpefely3r0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefely3r0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7e9f59k4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7e9f59k4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4nhka4a5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4nhka4a5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmoa72plw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmoa72plw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpslsqkcu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpslsqkcu3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplzngfraw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzngfraw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpejwsr07e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejwsr07e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp3ij2gx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp3ij2gx5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmparq7sxos/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmparq7sxos/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvkc97yb_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkc97yb_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm3brts3z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3brts3z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48pm5o9p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48pm5o9p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr1cvpi_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1cvpi_q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr02ivizs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr02ivizs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3rdo728e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3rdo728e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphkz5vhvb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkz5vhvb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq3qvov6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3qvov6j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7x1pelzb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7x1pelzb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppswzmv_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppswzmv_i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2l3kc2sm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2l3kc2sm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02yuwerq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02yuwerq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcrjhf5l9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcrjhf5l9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvm95vzv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvm95vzv_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ii2evbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ii2evbg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz7lk6nor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7lk6nor/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqg0pbj9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqg0pbj9j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4jvm8jqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jvm8jqs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm19yad1r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm19yad1r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4q7j0115/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4q7j0115/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6sn4hecl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sn4hecl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpunne4fpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunne4fpl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2h_tkvqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2h_tkvqt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2p_eqap6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2p_eqap6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_xxryexx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_xxryexx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8jsncegc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jsncegc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph61urrpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph61urrpi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzqzoag5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqzoag5n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3rfb3f2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3rfb3f2h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ze2t8k8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ze2t8k8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp41nufa_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41nufa_j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe6nqlhgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6nqlhgd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq7up5axw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq7up5axw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwwki3mfl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwki3mfl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvf7dcu4q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvf7dcu4q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0wm73oyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0wm73oyy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ot907lm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ot907lm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj7og_1sv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7og_1sv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2rd_2au_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2rd_2au_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu5q1k2eh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5q1k2eh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxogw503d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxogw503d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnlkh4c1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlkh4c1j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_soks93/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_soks93/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz4y0xblz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4y0xblz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiecql6zw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiecql6zw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp45way4cn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45way4cn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa0ptiimx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0ptiimx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwjxy1sel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjxy1sel/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0c8685e5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0c8685e5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ykoex3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ykoex3r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp820e5jvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp820e5jvi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz_e8n5bh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_e8n5bh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbpjonxt8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpjonxt8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv5skdpz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5skdpz7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx218hvu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx218hvu9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgzuz5_wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzuz5_wv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvf3lvelz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvf3lvelz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppwyiyz1x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwyiyz1x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1okhugt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1okhugt9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmum_t1r3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmum_t1r3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx5si3ozh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx5si3ozh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp30yw22yr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp30yw22yr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_070lymm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_070lymm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3uey763j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3uey763j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoipfco8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoipfco8a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpesktm8my/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesktm8my/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpihhwxw6c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihhwxw6c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxbwjg38g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxbwjg38g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr4az4g1r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr4az4g1r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzajwjanz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzajwjanz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpog6_y0uv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpog6_y0uv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpasrv0svw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasrv0svw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkyzicv72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyzicv72/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl66wmdqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl66wmdqj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqs5awro0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqs5awro0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp19frj1ol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19frj1ol/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf7n2z6at/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf7n2z6at/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0n28m7tg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0n28m7tg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphgvxoyri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgvxoyri/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpea9byaq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea9byaq4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp07tzbsf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07tzbsf3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qkutvyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qkutvyu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1q_3h4_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q_3h4_u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp304tzzps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp304tzzps/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx7foezxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7foezxj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe59az1ou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe59az1ou/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2e_px4dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2e_px4dk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmz0w469j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmz0w469j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6f0qeieb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6f0qeieb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2o19xjoa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2o19xjoa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ui3dl05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ui3dl05/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxl0j_szo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxl0j_szo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeg32g51t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeg32g51t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0m_8y0x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0m_8y0x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoftfgfnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoftfgfnb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyx0beyn9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyx0beyn9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphye4jv37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphye4jv37/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphnb9anv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphnb9anv5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ul3fk8y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ul3fk8y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzvc5stgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvc5stgr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy2a1xxog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2a1xxog/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwexdrkr8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwexdrkr8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1brqsjh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1brqsjh5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpom511751/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpom511751/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvilwdeah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvilwdeah/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprk032dvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprk032dvz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5us0czy_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5us0czy_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmlzjbzzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlzjbzzx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3b4sk_b_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3b4sk_b_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxz9cbj86/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxz9cbj86/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp40zrvajq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40zrvajq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcngwoix7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcngwoix7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjgov0uaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgov0uaj/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain57-method_chain57] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain24-method_chain24] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 2050 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4149876 | 4150133 | a | 0 | + | E | chr1 | 4149876 | 4150133 | a | 0 | + | E | chr1 | 4149876 | 4150133 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 190 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RjZWRmYARCBm4QYcPOwMDAKMVSksMox8rmxegmP+cSWJqRQdE+qJiBE6gGqICdiZGBmZGREQCUCgTs') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________________ test_subtraction[False] ____________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi0sshbfq/f1.bed -b /tmp/tmpi0sshbfq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkl2_uxq_/f1.bed -b /tmp/tmpkl2_uxq_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnz3ngvi9/f1.bed -b /tmp/tmpnz3ngvi9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdf5fe4lc/f1.bed -b /tmp/tmpdf5fe4lc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcnz1yftk/f1.bed -b /tmp/tmpcnz1yftk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxsprw_zz/f1.bed -b /tmp/tmpxsprw_zz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpf8_m3g4c/f1.bed -b /tmp/tmpf8_m3g4c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp97x944et/f1.bed -b /tmp/tmp97x944et/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6riis3ix/f1.bed -b /tmp/tmp6riis3ix/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzl4lf9zi/f1.bed -b /tmp/tmpzl4lf9zi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1wc2nq5k/f1.bed -b /tmp/tmp1wc2nq5k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnsd1mrfh/f1.bed -b /tmp/tmpnsd1mrfh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwfw80wzw/f1.bed -b /tmp/tmpwfw80wzw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2d6l5itk/f1.bed -b /tmp/tmp2d6l5itk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc2veb7v_/f1.bed -b /tmp/tmpc2veb7v_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplkzlwchg/f1.bed -b /tmp/tmplkzlwchg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3mwmqpws/f1.bed -b /tmp/tmp3mwmqpws/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpm2i5bpa4/f1.bed -b /tmp/tmpm2i5bpa4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpeecayyo9/f1.bed -b /tmp/tmpeecayyo9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxfc09hhc/f1.bed -b /tmp/tmpxfc09hhc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpq7ecgvtz/f1.bed -b /tmp/tmpq7ecgvtz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8zb7f9g0/f1.bed -b /tmp/tmp8zb7f9g0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkgyiqg_q/f1.bed -b /tmp/tmpkgyiqg_q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmm6g278e/f1.bed -b /tmp/tmpmm6g278e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfu7whnu2/f1.bed -b /tmp/tmpfu7whnu2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp942owiia/f1.bed -b /tmp/tmp942owiia/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcpxyqzz8/f1.bed -b /tmp/tmpcpxyqzz8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx4gdode4/f1.bed -b /tmp/tmpx4gdode4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprdat09h0/f1.bed -b /tmp/tmprdat09h0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmrjtz1sr/f1.bed -b /tmp/tmpmrjtz1sr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8vj6_j56/f1.bed -b /tmp/tmp8vj6_j56/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpb9dpdvqa/f1.bed -b /tmp/tmpb9dpdvqa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzza8z4j5/f1.bed -b /tmp/tmpzza8z4j5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplh155nap/f1.bed -b /tmp/tmplh155nap/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpj2zmpwtf/f1.bed -b /tmp/tmpj2zmpwtf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzrn6ciu5/f1.bed -b /tmp/tmpzrn6ciu5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp70gxdjdo/f1.bed -b /tmp/tmp70gxdjdo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn3g7iay1/f1.bed -b /tmp/tmpn3g7iay1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpe5r3at1o/f1.bed -b /tmp/tmpe5r3at1o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2n7xzti5/f1.bed -b /tmp/tmp2n7xzti5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5as4ew0a/f1.bed -b /tmp/tmp5as4ew0a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpehcsl4m7/f1.bed -b /tmp/tmpehcsl4m7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphnwofv85/f1.bed -b /tmp/tmphnwofv85/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqit8tgg0/f1.bed -b /tmp/tmpqit8tgg0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppa3r5cjd/f1.bed -b /tmp/tmppa3r5cjd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzo2fh6jo/f1.bed -b /tmp/tmpzo2fh6jo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv5i0qu8i/f1.bed -b /tmp/tmpv5i0qu8i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphzs_pp9a/f1.bed -b /tmp/tmphzs_pp9a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyqeql8aj/f1.bed -b /tmp/tmpyqeql8aj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7x6m2rpf/f1.bed -b /tmp/tmp7x6m2rpf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpm5p38xso/f1.bed -b /tmp/tmpm5p38xso/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzulswpos/f1.bed -b /tmp/tmpzulswpos/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpww1h6am6/f1.bed -b /tmp/tmpww1h6am6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpglp2pbs2/f1.bed -b /tmp/tmpglp2pbs2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpop8z2yxt/f1.bed -b /tmp/tmpop8z2yxt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8ejb953j/f1.bed -b /tmp/tmp8ejb953j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp336cfhb5/f1.bed -b /tmp/tmp336cfhb5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpb8c1m99m/f1.bed -b /tmp/tmpb8c1m99m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphvqgzwyb/f1.bed -b /tmp/tmphvqgzwyb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpq5of5zbv/f1.bed -b /tmp/tmpq5of5zbv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwau20i5m/f1.bed -b /tmp/tmpwau20i5m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuh9_kb8j/f1.bed -b /tmp/tmpuh9_kb8j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphx48j693/f1.bed -b /tmp/tmphx48j693/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmfx_nz_j/f1.bed -b /tmp/tmpmfx_nz_j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp67twteix/f1.bed -b /tmp/tmp67twteix/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_hjsn7y0/f1.bed -b /tmp/tmp_hjsn7y0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprp9b5rpb/f1.bed -b /tmp/tmprp9b5rpb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdw5yvjdn/f1.bed -b /tmp/tmpdw5yvjdn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp01kr8q5q/f1.bed -b /tmp/tmp01kr8q5q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcpbmrwg2/f1.bed -b /tmp/tmpcpbmrwg2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn48csv23/f1.bed -b /tmp/tmpn48csv23/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkhoqckyf/f1.bed -b /tmp/tmpkhoqckyf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_bh8nl9u/f1.bed -b /tmp/tmp_bh8nl9u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo77n4fpd/f1.bed -b /tmp/tmpo77n4fpd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpq31lhmpi/f1.bed -b /tmp/tmpq31lhmpi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsx0eg41t/f1.bed -b /tmp/tmpsx0eg41t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpaihvrecp/f1.bed -b /tmp/tmpaihvrecp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp04h0b7jm/f1.bed -b /tmp/tmp04h0b7jm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp87g4xdq5/f1.bed -b /tmp/tmp87g4xdq5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpj8k55jyb/f1.bed -b /tmp/tmpj8k55jyb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp06viwnnm/f1.bed -b /tmp/tmp06viwnnm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgtudjq8a/f1.bed -b /tmp/tmpgtudjq8a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbq8jhl12/f1.bed -b /tmp/tmpbq8jhl12/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7aetghfa/f1.bed -b /tmp/tmp7aetghfa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpq2xvvq1h/f1.bed -b /tmp/tmpq2xvvq1h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgjvcmbfd/f1.bed -b /tmp/tmpgjvcmbfd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph8z7wumc/f1.bed -b /tmp/tmph8z7wumc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpop5c8r4v/f1.bed -b /tmp/tmpop5c8r4v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpz7sgiwyo/f1.bed -b /tmp/tmpz7sgiwyo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9uz1s0h5/f1.bed -b /tmp/tmp9uz1s0h5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvobzc0q1/f1.bed -b /tmp/tmpvobzc0q1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6mzchzau/f1.bed -b /tmp/tmp6mzchzau/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyzn5_6au/f1.bed -b /tmp/tmpyzn5_6au/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpm0y2nu4g/f1.bed -b /tmp/tmpm0y2nu4g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2hpes9xx/f1.bed -b /tmp/tmp2hpes9xx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfz_zb5g1/f1.bed -b /tmp/tmpfz_zb5g1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9b2df4_a/f1.bed -b /tmp/tmp9b2df4_a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_exdleb5/f1.bed -b /tmp/tmp_exdleb5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvohc5zht/f1.bed -b /tmp/tmpvohc5zht/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp278vdu49/f1.bed -b /tmp/tmp278vdu49/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkof088ka/f1.bed -b /tmp/tmpkof088ka/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkdyp7piy/f1.bed -b /tmp/tmpkdyp7piy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprklmsyo5/f1.bed -b /tmp/tmprklmsyo5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1v_mdpim/f1.bed -b /tmp/tmp1v_mdpim/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1aq5ormm/f1.bed -b /tmp/tmp1aq5ormm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmporb5dkwu/f1.bed -b /tmp/tmporb5dkwu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpoepr57eo/f1.bed -b /tmp/tmpoepr57eo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwn54owfu/f1.bed -b /tmp/tmpwn54owfu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbxda6nl4/f1.bed -b /tmp/tmpbxda6nl4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa2cbd2uj/f1.bed -b /tmp/tmpa2cbd2uj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpq0sfdlsj/f1.bed -b /tmp/tmpq0sfdlsj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpacwujn_q/f1.bed -b /tmp/tmpacwujn_q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkp4y1gse/f1.bed -b /tmp/tmpkp4y1gse/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp565uut4r/f1.bed -b /tmp/tmp565uut4r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphiax8qda/f1.bed -b /tmp/tmphiax8qda/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgjzjp7ma/f1.bed -b /tmp/tmpgjzjp7ma/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpr1cknhwm/f1.bed -b /tmp/tmpr1cknhwm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpe_cdgzxe/f1.bed -b /tmp/tmpe_cdgzxe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqsfsrjto/f1.bed -b /tmp/tmpqsfsrjto/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6j2qb66w/f1.bed -b /tmp/tmp6j2qb66w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv7q2xriy/f1.bed -b /tmp/tmpv7q2xriy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3b7ba25w/f1.bed -b /tmp/tmp3b7ba25w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpswtznrwa/f1.bed -b /tmp/tmpswtznrwa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpaoy2vm7o/f1.bed -b /tmp/tmpaoy2vm7o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpz5cbec4e/f1.bed -b /tmp/tmpz5cbec4e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu9gcp5ou/f1.bed -b /tmp/tmpu9gcp5ou/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy47brji7/f1.bed -b /tmp/tmpy47brji7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprkiy8ixy/f1.bed -b /tmp/tmprkiy8ixy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi702cs_z/f1.bed -b /tmp/tmpi702cs_z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpm_1nvql_/f1.bed -b /tmp/tmpm_1nvql_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2tp80s2h/f1.bed -b /tmp/tmp2tp80s2h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2cenkud2/f1.bed -b /tmp/tmp2cenkud2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpleswnljw/f1.bed -b /tmp/tmpleswnljw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc63hhgkm/f1.bed -b /tmp/tmpc63hhgkm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpybju55rs/f1.bed -b /tmp/tmpybju55rs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgr_jcpkl/f1.bed -b /tmp/tmpgr_jcpkl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv_42j5jd/f1.bed -b /tmp/tmpv_42j5jd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp970kj5oy/f1.bed -b /tmp/tmp970kj5oy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3s33kp7l/f1.bed -b /tmp/tmp3s33kp7l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_1knrqoe/f1.bed -b /tmp/tmp_1knrqoe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp67o3b0hi/f1.bed -b /tmp/tmp67o3b0hi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi0p8p6n0/f1.bed -b /tmp/tmpi0p8p6n0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxmpeqk0l/f1.bed -b /tmp/tmpxmpeqk0l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0ded4__e/f1.bed -b /tmp/tmp0ded4__e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn1jjqc2t/f1.bed -b /tmp/tmpn1jjqc2t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpejee4slt/f1.bed -b /tmp/tmpejee4slt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxq89xdh_/f1.bed -b /tmp/tmpxq89xdh_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9vvhyxyg/f1.bed -b /tmp/tmp9vvhyxyg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9nd2lcdj/f1.bed -b /tmp/tmp9nd2lcdj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjnv24_1_/f1.bed -b /tmp/tmpjnv24_1_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnd6x3g64/f1.bed -b /tmp/tmpnd6x3g64/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnk9seet_/f1.bed -b /tmp/tmpnk9seet_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp26509kbl/f1.bed -b /tmp/tmp26509kbl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpoezkl8so/f1.bed -b /tmp/tmpoezkl8so/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppf9791np/f1.bed -b /tmp/tmppf9791np/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1z6jfk05/f1.bed -b /tmp/tmp1z6jfk05/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqqag507i/f1.bed -b /tmp/tmpqqag507i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_mfj7t_e/f1.bed -b /tmp/tmp_mfj7t_e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk0tfv0g_/f1.bed -b /tmp/tmpk0tfv0g_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpaaml0ujt/f1.bed -b /tmp/tmpaaml0ujt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpoolt7yq2/f1.bed -b /tmp/tmpoolt7yq2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain58-method_chain58] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ___________________ test_k_nearest[upstream-True-same-last] ____________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGOGBEYsPFAACYAAY=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu5eqe88g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5eqe88g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp278c66pp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp278c66pp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpto3l4bcl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto3l4bcl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp159sb_y_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp159sb_y_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_y8ozbzv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_y8ozbzv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4jtj7awb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jtj7awb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvpwipktz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvpwipktz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfqcpv7ct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqcpv7ct/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsx_6hhmk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsx_6hhmk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl1nmlt5s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl1nmlt5s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw1pjolnu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1pjolnu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplt8n1grg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplt8n1grg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmb6omkcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmb6omkcn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo2grkync/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2grkync/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvvr_32la/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvvr_32la/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2chuyw61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2chuyw61/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq9y11jtf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9y11jtf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg8_5igx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8_5igx6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxl8e33ht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxl8e33ht/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgxsw1uuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgxsw1uuo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2wz2oqef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wz2oqef/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg5z533sy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5z533sy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2g7mrsso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2g7mrsso/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnfaamv3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfaamv3k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz_n9yqno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_n9yqno/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiblyy8g6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiblyy8g6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpirbcv_n5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpirbcv_n5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplzz6j14f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzz6j14f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymew9qx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymew9qx6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwwdqpj5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwdqpj5c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8zxkpkpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8zxkpkpz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdlfxwlp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlfxwlp0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpolm3y7fh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpolm3y7fh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9wfpq_zq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9wfpq_zq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5c18s1ap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5c18s1ap/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9s1yp_vj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9s1yp_vj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghyb62o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghyb62o0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa7ymmd9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7ymmd9y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxf7lnbh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxf7lnbh2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2h0bqubu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2h0bqubu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj8tgnhmc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8tgnhmc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_0zmaboc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_0zmaboc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa7bba4hx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7bba4hx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxtv71wa3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxtv71wa3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdodigyf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdodigyf7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvozykqzt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvozykqzt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps8ox3p7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8ox3p7p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpie2jk52j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpie2jk52j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppsf4hq_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppsf4hq_e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc6osfqdk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6osfqdk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph3lk_8oe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3lk_8oe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptwvzturb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptwvzturb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpce4h6siu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpce4h6siu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6drg582i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6drg582i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpesh1hckh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesh1hckh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2g40crwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2g40crwm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02d6q528/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02d6q528/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpynosczib/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpynosczib/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprq6i51gw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprq6i51gw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2y_fclc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2y_fclc7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfzr8gyw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzr8gyw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8cf9c3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8cf9c3_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbo576ncv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbo576ncv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxytysvu0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxytysvu0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc6wj736t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6wj736t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq5rvop3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq5rvop3b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdawp734i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdawp734i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjycnueaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjycnueaf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0gop8p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0gop8p2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpni9475ax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpni9475ax/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbp553xov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbp553xov/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2b7nqw7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2b7nqw7z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaxrh9q9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxrh9q9l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_kidn3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_kidn3p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplt1jd3hl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplt1jd3hl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkc4kj55v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkc4kj55v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjp2q1vt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjp2q1vt1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfeunv4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfeunv4_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe46ciz82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe46ciz82/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfqsw11zn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqsw11zn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0c8f_l_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0c8f_l_4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8r_nshz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8r_nshz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg5n180zw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5n180zw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppf_vtbel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppf_vtbel/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbj9rokkr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbj9rokkr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkb2lim7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkb2lim7q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpawh9q273/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpawh9q273/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ior51o9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ior51o9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmigx3dyk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmigx3dyk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphy19prot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphy19prot/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8t0acp_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8t0acp_2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9afdyr41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9afdyr41/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphq1xrnna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphq1xrnna/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfzfbz9nz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzfbz9nz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp77g_7irp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77g_7irp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptyxw_1_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptyxw_1_q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvaka9jyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvaka9jyp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprzjcx6a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzjcx6a_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp55ndabka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55ndabka/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb188kikj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb188kikj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1g_vsjvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1g_vsjvi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc5h2nhfk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5h2nhfk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx4sv6xoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx4sv6xoh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2d__w1nd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d__w1nd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_yphrjdt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_yphrjdt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpowbpoa6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpowbpoa6q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphxvqok1g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxvqok1g/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain25-method_chain25] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 770 | 1028 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | + | E | chr1 | 1 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY4xwsmVgYGAEQmZGIA3CafqKOxjTQYJgcQYYBVTCwMLJx8gIAGWgAt4=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_k_nearest[upstream-True-False-last] ___________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = 'upstream', overlap = True, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how='upstream', E overlap=True, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp98ta2o2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98ta2o2l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyahhbi8i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyahhbi8i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2r6rcsdx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2r6rcsdx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2kp4usi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2kp4usi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwyayixrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwyayixrn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplxph_umt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplxph_umt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl7t94awf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7t94awf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpedpe4b0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedpe4b0a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp91qrkx26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91qrkx26/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpur4_77qs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpur4_77qs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi4k8rucw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4k8rucw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1yl4i2z5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1yl4i2z5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7z49fw08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7z49fw08/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd6i72br7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6i72br7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvlez9ylp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvlez9ylp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2x9gaxpr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2x9gaxpr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmcxregkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcxregkl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4r4h64_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4r4h64_b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnw830qut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnw830qut/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6grzz55j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6grzz55j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm0_ul7ub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0_ul7ub/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjtpsz39j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjtpsz39j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8jgoa1ab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jgoa1ab/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxoucjzn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxoucjzn8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpda4fc3b_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpda4fc3b_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp43rae2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp43rae2d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv0p9qjnm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv0p9qjnm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7kzgwj2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7kzgwj2h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzyyrjclz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyyrjclz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48t1k1_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48t1k1_x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpflse132x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflse132x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeui4egi2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeui4egi2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmv0c1xac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmv0c1xac/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn0hn316f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0hn316f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppueuex21/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppueuex21/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvpq0bwaq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvpq0bwaq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__ptlc00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__ptlc00/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppnu8c4w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppnu8c4w9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp89iu6m_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp89iu6m_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0r8nfumk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0r8nfumk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdxso64c7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxso64c7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7plynj2p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7plynj2p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbdpuqr4q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbdpuqr4q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiv1ca1tw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiv1ca1tw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgsdrij79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgsdrij79/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ________________________ test_nearest[None-True-False] _________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 59 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGBEoqBsAACRAAY=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 | (and 459 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5gc0u1w8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gc0u1w8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpds5as471/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpds5as471/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9j_g0ba6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9j_g0ba6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6eig1nc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6eig1nc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 2 chr6 65796 69858 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65796 | 73477 | a | 0 | ... | | chr1 | 65796 | 75796 | a | 0 | ... | | chr6 | 65796 | 69858 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr6 65796 69858 + 0 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 df2 Chromosome Start End Strand Distance 2 chr6 65796 69858 + 0 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 Actual Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 2 chr6 65796 69858 + 0 Expected Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 2 chr6 65796 69858 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4fatly02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4fatly02/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65796 | 73477 | a | 0 | ... | | chr1 | 65796 | 75796 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 df2 Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 Actual Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 Expected Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzbjcf2q9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzbjcf2q9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65796 | 73477 | a | 0 | ... | | chr1 | 65796 | 75796 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 df2 Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 Actual Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 Expected Chromosome Start End Strand Distance 0 chr1 65796 73477 + 0 1 chr1 65796 75796 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjt6_qf65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt6_qf65/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoirdrd6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoirdrd6i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuoqtu4z3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuoqtu4z3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqibutok5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqibutok5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppt_r5q8m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppt_r5q8m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj3x_i9s2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3x_i9s2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpifejibuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpifejibuf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp82sjiecd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82sjiecd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfm2s7cku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfm2s7cku/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf_zuj7oc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_zuj7oc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx62dgnxh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx62dgnxh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjg1zifsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjg1zifsn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ydhlsgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ydhlsgr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptbemrjvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbemrjvf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4tkceyi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tkceyi7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp19keoub2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19keoub2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7xplq6w0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xplq6w0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7tb9jsh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7tb9jsh0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8ez3vg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8ez3vg9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppdgvdr8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdgvdr8p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0orh_j1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0orh_j1i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa0gjjb97/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0gjjb97/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpblv1n1qr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpblv1n1qr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkm6zh7af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkm6zh7af/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwgdgnhw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwgdgnhw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy0emaol4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0emaol4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptra236rz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptra236rz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp725msbly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp725msbly/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpda2owsvp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpda2owsvp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppbwvgb5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbwvgb5u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qhw3ubl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qhw3ubl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy4f_qcqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4f_qcqo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsnif9vt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsnif9vt9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2hqs2ide/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hqs2ide/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv042k_s6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv042k_s6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9m6swmjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9m6swmjv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbfc9bs7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbfc9bs7g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxzhl32mi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxzhl32mi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbbicj8d0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbicj8d0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1910bg34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1910bg34/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5djvs2zk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5djvs2zk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmsbgqira/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsbgqira/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3brcpvvb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3brcpvvb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps3ijb669/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3ijb669/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_52x2o9x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_52x2o9x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz1sry5b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz1sry5b3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjyq056qt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjyq056qt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9n5b2k0r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9n5b2k0r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg329zkfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg329zkfi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp161lk1ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp161lk1ig/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpodf598x6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodf598x6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpumffxtvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumffxtvz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp53et1yu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53et1yu3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy5kynoxu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5kynoxu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphfhc4vso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphfhc4vso/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1sl3ribl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sl3ribl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn337zto7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn337zto7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_1he2fus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1he2fus/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4gs0qn_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4gs0qn_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwxrcoszk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxrcoszk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpghstn177/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghstn177/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqyhqqpqk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqyhqqpqk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw3xg15_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3xg15_j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ggrnqcz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ggrnqcz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3bdgwohx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bdgwohx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxl068ioc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxl068ioc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppdiivec5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdiivec5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq4aiizds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq4aiizds/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpazb3opj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazb3opj3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnzc6wld_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnzc6wld_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjo5m4at2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjo5m4at2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8s212xy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8s212xy2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprra9gchr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprra9gchr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyenawgl1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyenawgl1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9_tfrhi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9_tfrhi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkr96q0e4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkr96q0e4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfox59nav/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfox59nav/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_rp5d95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_rp5d95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbd58hwwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbd58hwwo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain59-method_chain59] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain26-method_chain26] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 7326574 | 7333704 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 257 | 514 | a | 0 | - | | | chr1 | 257 | 514 | a | 0 | - | | | chr1 | 257 | 514 | a | 0 | - | | | chr1 | 257 | 514 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 136 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2fRUWXfyAACMfmnc/kYKi3D9VWkbzIwgsUYGZkY2UFsdhaDZlZtprDv8QEfGTgYGXkZuYGibHxAzMDLxCjMyCgPUs8E1gfEjABHFwno') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65824 | 66081 | a | 0 | + | | | chr1 | 65824 | 65827 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 917505 | 918019 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 169 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYzVg0VFlZ2QAAR5GRgZGBk5GRnkmBiATyGZiZ2BgBjLZyuMDPjJwAEUY2PiAmIGXCaQUrI0JTDEyAACDrgM1') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_k_nearest[None-False-opposite-last] ___________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = 'opposite', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness='opposite', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4175490 | 4175544 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 135938 | 139963 | a | 0 | + | E | chr1 | 262159 | 266184 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2TgYQACRgYG+22NQIYpiB3Izs7IwCgCxCAIlGNh4GNgYRJmZBDk3wESYwAAYkYDOw==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgpxvbiw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpxvbiw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp104o2u5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp104o2u5e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpum45tgoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpum45tgoz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptw8308m7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptw8308m7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1rjrldvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rjrldvq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbmdz9i9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmdz9i9l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzba25gta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzba25gta/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp554mfnl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp554mfnl9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6fbh6czt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6fbh6czt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmzj7bcpu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzj7bcpu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprepm_0le/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprepm_0le/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qcrsm7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qcrsm7r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe0h912ur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0h912ur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg987zn0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg987zn0e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdo_3s46n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdo_3s46n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg78y772j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg78y772j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgeg6aqt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgeg6aqt7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjp68e8k2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjp68e8k2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ra6d6so/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ra6d6so/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp88084jos/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp88084jos/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprc0z83nr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprc0z83nr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvf463z_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvf463z_5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwiqhpok7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwiqhpok7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphackah3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphackah3y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_p_ne0ly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_p_ne0ly/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7efxck49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7efxck49/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc6979sgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6979sgu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjl7sywqf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjl7sywqf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplbl95tzo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbl95tzo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzao0cffr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzao0cffr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgr0a8pes/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgr0a8pes/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6dutbcci/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6dutbcci/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1arpuq98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1arpuq98/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp85rtv6yz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85rtv6yz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxtkk_z7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxtkk_z7x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt1u1gibv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1u1gibv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_f9mu5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_f9mu5e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp46nvxryp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46nvxryp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi4h7501r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4h7501r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn6pyc6_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6pyc6_n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy0w9x71a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0w9x71a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdcnu75uv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcnu75uv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9sxw_4xx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9sxw_4xx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbp1iazxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbp1iazxo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn8pixdw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8pixdw4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpreip6h9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpreip6h9y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7gm1ywx8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7gm1ywx8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpctdquvex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctdquvex/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp82486yyi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82486yyi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzaou_gvu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzaou_gvu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0knpr2_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0knpr2_b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxqo2gvfz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqo2gvfz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp87l9gm07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87l9gm07/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzen8liwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzen8liwo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqvzmf0xf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvzmf0xf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp71hmj5pl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp71hmj5pl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfcpl_isq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcpl_isq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhqpg05u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhqpg05u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmd3xf8dt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmd3xf8dt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq61nz_rr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq61nz_rr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyc81lvhe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyc81lvhe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpupvza84d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupvza84d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4k_8fu_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4k_8fu_d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmqpl7pfk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqpl7pfk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpehrxndk1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehrxndk1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp05wl63l7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05wl63l7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdm4pk394/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdm4pk394/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj1t1_sem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1t1_sem/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgjhxiguo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjhxiguo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyso50qxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyso50qxo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpygzpluhm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygzpluhm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2n523e7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2n523e7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp792hta7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp792hta7z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpray6oevn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpray6oevn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbi805vhm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbi805vhm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp74zprsii/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74zprsii/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7l_1q8ti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7l_1q8ti/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk92xlayb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk92xlayb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfvumlsmc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvumlsmc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5piyl0_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5piyl0_d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiqink0d5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqink0d5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyc7oxpfk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyc7oxpfk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyjirbgmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyjirbgmv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0w_ar4c1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0w_ar4c1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuf_mjz77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuf_mjz77/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkgirpgg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkgirpgg5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1g6csjje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1g6csjje/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpotcldvuv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpotcldvuv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp83rlt4ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp83rlt4ip/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpav4o_o9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpav4o_o9r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnoej1lp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnoej1lp4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph_y_4bdn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_y_4bdn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl92yimqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl92yimqo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_ruv8df/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_ruv8df/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpufbinkg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufbinkg9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu_kg0dzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_kg0dzw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuchf_w_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuchf_w_w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp25iewcka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25iewcka/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmo6w3oyb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo6w3oyb/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________________ test_nearest[None-True-same] _________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 123 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGBEoqBsAACRAAY=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 464 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps27efdz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps27efdz4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu2d41972/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2d41972/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5iexz0oe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5iexz0oe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxdikr2oq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdikr2oq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj47a6k9p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj47a6k9p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpembkwo0q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpembkwo0q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmlgq1yn9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlgq1yn9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnloass60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnloass60/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppe3td7d2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe3td7d2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65547 - 0 1 chr1 8719343 8719344 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8719343 | 8719344 | a | 0 | ... | | chr1 | 65537 | 65547 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 65537 65547 - 0 0 chr1 8719343 8719344 + 0 df2 Chromosome Start End Strand Distance 0 chr1 65537 65547 - 0 1 chr1 8719343 8719344 + 0 Actual Chromosome Start End Strand Distance 0 chr1 65537 65547 - 0 1 chr1 8719343 8719344 + 0 Expected Chromosome Start End Strand Distance 0 chr1 65537 65547 - 0 1 chr1 8719343 8719344 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdl2s4ji1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdl2s4ji1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1npd97fq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1npd97fq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpebp8i81t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebp8i81t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5g3yeu4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5g3yeu4h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7nllz9j0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nllz9j0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj6qx39n8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj6qx39n8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppnku998b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppnku998b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphnh_t4sl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphnh_t4sl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppk7bbec4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppk7bbec4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwpf2ooq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpf2ooq2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpudbwhjch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudbwhjch/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcjzp7xb3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjzp7xb3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9mio1yql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mio1yql/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj05rghl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj05rghl6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ev_my8q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ev_my8q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_tb16d8i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tb16d8i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuojz6okp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuojz6okp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp045qenyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp045qenyq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjr38abke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjr38abke/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2b21773l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2b21773l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9pujkzl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9pujkzl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpefnr67pn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefnr67pn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi7bllpdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7bllpdq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiae6xui3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiae6xui3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi50ake3v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi50ake3v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnzlg8moa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnzlg8moa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0oq15ihb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0oq15ihb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgdlyvjvg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdlyvjvg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7njnu4p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7njnu4p2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3caap9ky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3caap9ky/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp632mp_j9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp632mp_j9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7414 + 0 1 chr1 1 7414 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7414 | a | 0 | ... | | chr1 | 1 | 7414 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7414 + 0 1 chr1 1 7414 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 7414 + 0 1 chr1 1 7414 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7414 + 0 1 chr1 1 7414 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7414 + 0 1 chr1 1 7414 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnnnp2wt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnnnp2wt9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3k6613g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3k6613g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnv7_w_p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnv7_w_p4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmperwc333i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmperwc333i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpntz75rbe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpntz75rbe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplpr0bus_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpr0bus_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd5zkfh_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd5zkfh_2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw68y5she/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw68y5she/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ru6nvkp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ru6nvkp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6mkrl65r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mkrl65r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5n1yx_3m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5n1yx_3m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2qbbiqbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qbbiqbc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpofwq3g8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofwq3g8x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcqwz9t1b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqwz9t1b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmnwh40jz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmnwh40jz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpehg58lp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehg58lp0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ic8whk2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ic8whk2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpukt1_rig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukt1_rig/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmput0cgcjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmput0cgcjv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7eo3v3fi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7eo3v3fi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbg7bxyjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbg7bxyjo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp45t273m0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45t273m0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplsu9gqad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplsu9gqad/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6wo1lgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6wo1lgi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptv3wc10k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv3wc10k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcaw_4lhp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcaw_4lhp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5nzmhkh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5nzmhkh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcsy3vuxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcsy3vuxb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3cnyhwkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cnyhwkk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp357tofpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp357tofpz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vc7q1hy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vc7q1hy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2hpjhyjb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hpjhyjb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpasnqbayg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasnqbayg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5dx8bg9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5dx8bg9k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain60-method_chain60] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_k_nearest[None-False-same-last] _____________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt0mf5qox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0mf5qox/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5d39fzu1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5d39fzu1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph_ycgaot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_ycgaot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02zrg80r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02zrg80r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph6kcvhxm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6kcvhxm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_h3zxwpr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_h3zxwpr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_8wub7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_8wub7k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2tvy_bf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2tvy_bf8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpivy7dm10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivy7dm10/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2im4uui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2im4uui/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpee9p1bsy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpee9p1bsy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0mlai160/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0mlai160/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk469ni70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk469ni70/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7pbaar3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pbaar3b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb7n1uy1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7n1uy1j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4myp0_xy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4myp0_xy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36im97al/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36im97al/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuv7rj68x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuv7rj68x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0s8gjts_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0s8gjts_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4c3zt4qo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4c3zt4qo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9b895qy_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9b895qy_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0bbb6h57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0bbb6h57/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe3w5pw98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe3w5pw98/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7oyv9b_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7oyv9b_g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeggnvru3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeggnvru3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpac8pvkxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpac8pvkxf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7dzf2icx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dzf2icx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkwg_g4ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkwg_g4ox/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxnk0mslg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxnk0mslg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphy9rdygj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphy9rdygj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7c450wn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7c450wn0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5_zrsyf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5_zrsyf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp11fjcdus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11fjcdus/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpovvhunv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpovvhunv8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5poue84l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5poue84l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdomlvbmk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdomlvbmk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplxgfzb3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplxgfzb3w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1wb577ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wb577ua/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp685_7d9x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp685_7d9x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvxudlr47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvxudlr47/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_cj0zk35/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cj0zk35/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4znlfvkq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4znlfvkq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp06i7exdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06i7exdq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl533nw4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl533nw4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpto1y5to5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto1y5to5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp40bvl57b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40bvl57b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg6wvpa60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6wvpa60/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppb2ykdok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppb2ykdok/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ycqmmgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ycqmmgu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpty7blojx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpty7blojx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp381ifv3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp381ifv3j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp14wg3v_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp14wg3v_u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdkfvhxm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkfvhxm2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzuco9arp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzuco9arp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk42l3p5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk42l3p5g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi3ndojkq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3ndojkq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9im_6ou4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9im_6ou4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmizt_g8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmizt_g8x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqej5f4aq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqej5f4aq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfjy1y72k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjy1y72k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_iu0e077/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_iu0e077/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_vr7hyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_vr7hyj/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain27-method_chain27] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 67587 | a | 0 | - | E | chr1 | 983114 | 985164 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3407875 | 3411720 | a | 0 | + | E | chr1 | 68868 | 72713 | a | 0 | + | E | chr1 | 68868 | 72713 | a | 0 | + | E | chr1 | 68868 | 72713 | a | 0 | + | E | chr1 | 68868 | 72713 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicHYw7DkBAGITn2/WKEIWESEStFW6g0jmIC7iExKXUjuS3xbwymaG/n5Pxal4JlBhEpQ01qXkgC2wkHMOOK5mJVVt06ki9coUWrYucaenlq+jf2NdUcLSq+QDZ7gaf') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________ test_k_nearest[None-False-False-last] _____________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk7fhp6qm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7fhp6qm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptkg_gw65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkg_gw65/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmple68u3gk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmple68u3gk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_x3thbv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_x3thbv9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc82hmarh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc82hmarh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1ogxuk13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ogxuk13/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpel0qps3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpel0qps3k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpentfi4ex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpentfi4ex/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimb23zc4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimb23zc4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7x_l_y85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7x_l_y85/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6i6ru1p5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i6ru1p5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplg9s5l2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplg9s5l2m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_jsfamws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jsfamws/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8fzfdvyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8fzfdvyo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsqzb80s2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqzb80s2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvm_qfpo8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvm_qfpo8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpilgs6n7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpilgs6n7i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7459wlst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7459wlst/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdobcfylc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdobcfylc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmgh307gn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgh307gn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnlgtrrpj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlgtrrpj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwa4mlbk8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwa4mlbk8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiryz5327/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiryz5327/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpssshbr_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssshbr_e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppfu4cwgb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfu4cwgb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwpkwswbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpkwswbx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprmgs8je4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprmgs8je4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp64p0rfry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64p0rfry/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbl9xz_d7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbl9xz_d7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt7s6mtte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7s6mtte/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy2a9h0u4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2a9h0u4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8y829cqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8y829cqq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdgbi1v6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdgbi1v6q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph55ivvdx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph55ivvdx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4k0b_017/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4k0b_017/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwb_a9pc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwb_a9pc0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0xjga3ds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xjga3ds/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt2b5o8rq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2b5o8rq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbu68diks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu68diks/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm0fkbqn7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0fkbqn7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpma24gems/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma24gems/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_gs7b3y9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gs7b3y9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb9383h_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb9383h_x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgs6fql1h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgs6fql1h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplrkfv5fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplrkfv5fa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph_gudq25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_gudq25/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_rnbz5b_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_rnbz5b_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp07nrp44n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07nrp44n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt19g2dix/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt19g2dix/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv30i4lt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv30i4lt9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptln9z_yy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptln9z_yy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpszehpdbs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszehpdbs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9gran8bq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9gran8bq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpea83vxvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea83vxvf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi590hwwu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi590hwwu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_fmt0ftx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fmt0ftx/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. _______________________ test_nearest[None-True-opposite] _______________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 124 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGOGBkRBKCsgEApQAH') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 457 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqklldjc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqklldjc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnxthlf2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxthlf2d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpubuj3ocu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpubuj3ocu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9esdybx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9esdybx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpox940fqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpox940fqd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvju8qn6n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvju8qn6n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprxm3887_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxm3887_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6q84oenu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6q84oenu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qtvu1du/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qtvu1du/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpulmpzvvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpulmpzvvh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnk4mx63w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnk4mx63w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf663rn1p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf663rn1p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ww8svx_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ww8svx_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsthp5v6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsthp5v6m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3mag4byt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mag4byt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv9dqgeec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9dqgeec/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3c2_gjpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3c2_gjpl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ct3cn9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ct3cn9h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizzpy2ti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizzpy2ti/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8an0yxs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8an0yxs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8y_qkcmd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8y_qkcmd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkqx5x131/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkqx5x131/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 259 1288 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 259 | 1288 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 259 1288 + 0 df2 Chromosome Start End Strand Distance 0 chr1 259 1288 + 0 Actual Chromosome Start End Strand Distance 0 chr1 259 1288 + 0 Expected Chromosome Start End Strand Distance 0 chr1 259 1288 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3e1mfmr1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3e1mfmr1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy6hf3kb5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6hf3kb5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdwz63h0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwz63h0w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbc2oliv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc2oliv7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprrraxoe0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrraxoe0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgub3uicl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgub3uicl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5vsoa0ax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vsoa0ax/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw05fbxem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw05fbxem/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp03d7ygit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03d7ygit/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_5j33ra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_5j33ra/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaden714s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaden714s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwtasc5r2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwtasc5r2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpji4hsmlm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpji4hsmlm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpebax25op/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebax25op/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk9i62ftw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9i62ftw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp847db01d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp847db01d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpffblhoa2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffblhoa2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe0ww58c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0ww58c9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpys_4uyak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpys_4uyak/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj1ui34tm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1ui34tm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkvhz9m85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvhz9m85/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprjivguq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjivguq2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1bx0zkxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1bx0zkxr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8amksbwu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8amksbwu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2hb0zs5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hb0zs5v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpztby80y5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztby80y5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gycjiev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gycjiev/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdc77_c69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc77_c69/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp73hms46n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp73hms46n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu74_iddd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu74_iddd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphcdmdpf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcdmdpf3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6f168lc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6f168lc_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_f3cyvg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_f3cyvg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph920di_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph920di_u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg2i6gtea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2i6gtea/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpce58us3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpce58us3w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbwmmxkjw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbwmmxkjw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4iy4qc59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4iy4qc59/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt_en12uh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_en12uh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5wyrzefp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5wyrzefp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptrqryawl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrqryawl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz2ss6b46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz2ss6b46/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzrezczyh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrezczyh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdbwqlsyv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbwqlsyv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdnv7z461/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnv7z461/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv4v31xjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv4v31xjo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgunb3tjq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgunb3tjq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsufgoj5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsufgoj5p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj45cdkft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj45cdkft/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl7kxzgom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7kxzgom/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsefrg_cu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsefrg_cu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4p7vltpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4p7vltpn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_nppihym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_nppihym/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwgdag373/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwgdag373/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gl827qk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gl827qk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp63al8t0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp63al8t0y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpestsr0ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpestsr0ua/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxqt7f8ux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqt7f8ux/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvmcz0co7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmcz0co7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdcdr14xi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcdr14xi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4g1fg1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4g1fg1n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0rcm0nyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0rcm0nyd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp46qyfysr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46qyfysr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpapf85u9p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpapf85u9p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplfx8tfst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfx8tfst/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphip69wm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphip69wm3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1_ntces4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_ntces4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoq47tnb8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoq47tnb8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1282 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3mk061z2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mk061z2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqd_5dz_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd_5dz_p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn01vncj6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn01vncj6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ug1md84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ug1md84/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6i8uhexp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i8uhexp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6w_m0qwi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6w_m0qwi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj1ihc7pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1ihc7pf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdncj1bzm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdncj1bzm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmput5m_uw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmput5m_uw4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0vshbivl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0vshbivl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnfz8tx8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfz8tx8_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp50cidw0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50cidw0d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpids_5j61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpids_5j61/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5nq5bjw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5nq5bjw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpve8pk3dh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpve8pk3dh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppv96scxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppv96scxj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain61-method_chain61] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain28-method_chain28] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 215 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________________ test_nearest[None-False-False] ________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:110 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E (and 34 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp66geybj2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66geybj2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpksn9zmee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksn9zmee/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpivgax3q7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivgax3q7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy8r0loli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy8r0loli/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp42k0ogcu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42k0ogcu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp57juald3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57juald3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphb9nhpct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphb9nhpct/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gaj8brq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gaj8brq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3npqb8vn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3npqb8vn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6cpkt8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6cpkt8c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp641anu_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp641anu_c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9dsy39j2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9dsy39j2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4htzfflp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4htzfflp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnufsooe2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnufsooe2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkomg4was/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkomg4was/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi0ccugw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0ccugw4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7a9yxy3z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7a9yxy3z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiq47w3b4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiq47w3b4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg8fgm05n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8fgm05n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq62lt89a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq62lt89a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp31uzykcb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31uzykcb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5tx6qj67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5tx6qj67/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps9d1i0qu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9d1i0qu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp35vwex4i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35vwex4i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpli0ee4pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpli0ee4pb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzsd87xdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzsd87xdw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk5_5pymx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5_5pymx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppx8dmtpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppx8dmtpz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwmprcpcb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmprcpcb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1bjfk_4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1bjfk_4z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplksfntfy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplksfntfy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa5eiznaw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5eiznaw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpceva7l2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpceva7l2w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvsq8_wra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsq8_wra/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpixop12_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixop12_w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprdzhn9z1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdzhn9z1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpla_y5c0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpla_y5c0v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1lw7d14y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lw7d14y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpti_k2bmc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpti_k2bmc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy_oa3ywy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_oa3ywy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj_9yda2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_9yda2a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprhn02zwz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhn02zwz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu4avobid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu4avobid/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf97mnons/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf97mnons/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi688bu0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi688bu0s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3fiy915a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3fiy915a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe_o7fb1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_o7fb1u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmj4k8t9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmj4k8t9n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72j_880s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72j_880s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8h312hev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h312hev/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7may6hq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7may6hq2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxf5vrhuu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxf5vrhuu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2c2ff3kg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2c2ff3kg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptl_uu1ge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptl_uu1ge/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9tx22_lh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tx22_lh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpae2o9cvj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpae2o9cvj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpidica23x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidica23x/f2.bed) ___________________ test_k_nearest[None-True-opposite-last] ____________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = True, strandedness = 'opposite', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness='opposite', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpntb902a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpntb902a_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3j7u6pt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3j7u6pt7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp49krpk6s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp49krpk6s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmponf_zfcr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmponf_zfcr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpisrv2r0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpisrv2r0d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp72iupkir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72iupkir/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf976ly1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf976ly1c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4x00q0eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4x00q0eg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp15nlq1fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15nlq1fa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfqejn56n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqejn56n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp44dsax08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44dsax08/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa4ann775/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4ann775/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp1gekuod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1gekuod/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0hz6v723/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hz6v723/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpks0gqoei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpks0gqoei/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5eyrfqv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5eyrfqv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpte_q1fvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpte_q1fvf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpniapzwz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpniapzwz5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl8j7hzpw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8j7hzpw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuvu3b35b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuvu3b35b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0a_qavm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0a_qavm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpel2br9zz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpel2br9zz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptewhb6zs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptewhb6zs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp89vtjkui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89vtjkui/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdieh9awh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdieh9awh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__7m9_nj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__7m9_nj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps88eu2ax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps88eu2ax/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpesio5jrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesio5jrz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptgzerogr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptgzerogr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7a4f5ff7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7a4f5ff7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4hsj5p4l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4hsj5p4l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp08l53u6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08l53u6t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzum5ysy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzum5ysy8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdqk2fn5x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqk2fn5x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiyhuvpux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiyhuvpux/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_x8zk14c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_x8zk14c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp528h1gyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp528h1gyn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps_akpftj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_akpftj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6hz5mn3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hz5mn3_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjeijooms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjeijooms/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbzipzs4b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbzipzs4b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppmoh2_jy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmoh2_jy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ygj1e57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ygj1e57/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyszz189e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyszz189e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzgr0ka2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzgr0ka2v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6y0ft_i5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6y0ft_i5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcm8ljn6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcm8ljn6_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprln8ccxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprln8ccxt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8h8_59_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h8_59_m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi6t3kbfw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi6t3kbfw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0k3i3623/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0k3i3623/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmftfvh7n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmftfvh7n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgsaztuju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgsaztuju/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_mzjnw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_mzjnw5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdxnq5ovt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxnq5ovt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp07p3exj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07p3exj1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpto5lkhwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto5lkhwh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_egpyfl5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_egpyfl5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbcnmgj7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbcnmgj7p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdvoxifzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdvoxifzf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwvw8oavy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvw8oavy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5crhy8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5crhy8h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoz4bvhgn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz4bvhgn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe4bryf4f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4bryf4f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8v9rqg6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8v9rqg6d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaj7azs2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaj7azs2a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp14svg01j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp14svg01j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt748o6i4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt748o6i4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe02m4b1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe02m4b1n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgx2x5fz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgx2x5fz7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppty3sptq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppty3sptq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ozeuvan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ozeuvan/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjoup7vee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjoup7vee/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp75q7hztp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75q7hztp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsfbnteb9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfbnteb9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj64cyz0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj64cyz0j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmsso_x65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsso_x65/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp31riu541/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31riu541/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmxp9it7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxp9it7m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg7j2n1i4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7j2n1i4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphuoe7tn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphuoe7tn5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyznrlqlh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyznrlqlh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2fywfi8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2fywfi8j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqk280cam/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqk280cam/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvddp530b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvddp530b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4_7i2bo6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4_7i2bo6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpix_8raf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpix_8raf1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpris14eps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpris14eps/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2637i1wt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2637i1wt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm8x3vazn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8x3vazn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6gbifyf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6gbifyf3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3q5u28c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3q5u28c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqfg71fp_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqfg71fp_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgo4jgmym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgo4jgmym/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1pzekv1q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1pzekv1q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ubdq_gc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ubdq_gc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdookc8ow/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdookc8ow/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ________________________ test_nearest[None-False-same] _________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjb7bb5_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjb7bb5_l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ilihn_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ilihn_a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx8h4b0xe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8h4b0xe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn3ru1b95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3ru1b95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppny7005j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppny7005j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7kp5k160/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7kp5k160/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgty786kl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgty786kl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg_r40z6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_r40z6t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpts5u6cqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpts5u6cqy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_cv3n2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_cv3n2r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfr2tlyyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfr2tlyyn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpic3o5app/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpic3o5app/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3mn94hog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mn94hog/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0p798mdk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0p798mdk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmr_nah28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmr_nah28/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8rk_5phm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8rk_5phm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7j2cumjc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7j2cumjc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2jiv1ef0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jiv1ef0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqwubvic6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwubvic6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwnh91yab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwnh91yab/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5_wgoy4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_wgoy4o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxxks9f_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxks9f_8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5o3p1nqz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5o3p1nqz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpun8d39np/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpun8d39np/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12iis664/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12iis664/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmn0x3yi0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmn0x3yi0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp51zxbqbp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51zxbqbp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplubx6chw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplubx6chw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpndfduyfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndfduyfm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93ea925t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93ea925t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprk6m4nmp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprk6m4nmp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6d58s102/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6d58s102/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2wcy5327/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wcy5327/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprgb7bu9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgb7bu9j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpitnvbgd6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpitnvbgd6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc2y6xz74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2y6xz74/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph0gx7115/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph0gx7115/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbmz0y_31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmz0y_31/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7nty093h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nty093h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptjz2uevb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptjz2uevb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpip7liq6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpip7liq6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphppbx4gq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphppbx4gq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcjxn_ax9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjxn_ax9/f2.bed) ___________ test_three_in_a_row[strandedness_chain62-method_chain62] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_k_nearest[None-True-same-last] ______________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzalnvlzg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzalnvlzg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgd7bml1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgd7bml1n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn2g5kdmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn2g5kdmb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ahwhvpq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ahwhvpq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp72jefkv4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72jefkv4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0nggc78i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0nggc78i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo3jgpc5t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo3jgpc5t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ia0txrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ia0txrn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfdxdj3xw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdxdj3xw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnlcysq5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlcysq5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd0e6h6oq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0e6h6oq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ialnmmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ialnmmi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppbx0u58j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbx0u58j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgwftgqoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgwftgqoz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkp8zesk4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkp8zesk4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe5grj2ru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5grj2ru/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_bg8q5ec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_bg8q5ec/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc_p_mais/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_p_mais/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyr91w789/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyr91w789/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphbi2jsv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbi2jsv2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0oq9gcxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0oq9gcxk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppemv7iz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppemv7iz8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5vk5v2s2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vk5v2s2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg3mznxdk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3mznxdk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdoxtp9as/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdoxtp9as/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbdflh53_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbdflh53_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsw43o9h7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsw43o9h7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqvrq_8j5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvrq_8j5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiwbtfgyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiwbtfgyx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeiamwu5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeiamwu5d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ffjb2gi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ffjb2gi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpio518q0z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpio518q0z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2gmchgj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gmchgj4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1s014cgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1s014cgs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn41kbzqx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn41kbzqx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0a0w67yo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0a0w67yo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphgg5sr71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgg5sr71/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4t6kxmyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4t6kxmyt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbyr3ocix/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbyr3ocix/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp12na98lq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12na98lq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvz46fwqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvz46fwqo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpquddjtqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpquddjtqq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkrsz9k3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkrsz9k3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvx60dns3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvx60dns3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxs61gd71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxs61gd71/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmgido33d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgido33d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4vehl29z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4vehl29z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf690k36a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf690k36a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvd9c9yff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvd9c9yff/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpldp_0f79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldp_0f79/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain29-method_chain29] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 259 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1508668 | 1509461 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgYmBgBEJ2RkZGEAsCgLQESJgxOm7mRxBXUJzVmoGDWYKBAQAtUgL7') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_k_nearest[None-True-False-last] _____________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = True, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzknmyrpb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzknmyrpb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_w096t8y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_w096t8y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_4pl3htl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4pl3htl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg8ufanml/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8ufanml/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphqwzmegt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphqwzmegt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbclx5m15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbclx5m15/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmf3qa1y_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmf3qa1y_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps1as_br3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1as_br3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzavjqhmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzavjqhmv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg2xsjzto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2xsjzto/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5sf1_1f0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5sf1_1f0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ks7jp6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ks7jp6p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfd0u071_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfd0u071_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0uf_klrf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0uf_klrf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbrou_s42/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrou_s42/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdwklu84s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwklu84s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf45vzqpp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf45vzqpp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt21tcxig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt21tcxig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuub2ksua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuub2ksua/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplkmrtzc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplkmrtzc0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz77x6ac8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz77x6ac8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkdromzzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdromzzw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp35q11dh7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35q11dh7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9tmxflr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9tmxflr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0fx7e2rp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fx7e2rp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1j63urb7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1j63urb7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp0p4hc7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp0p4hc7m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplcy12yyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcy12yyr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7mfhfz9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mfhfz9w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ymahc__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ymahc__/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4jyjx2t2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jyjx2t2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsip7swqf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsip7swqf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9caksjkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9caksjkm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvyjirs5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvyjirs5n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptc7qwc30/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptc7qwc30/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbi7iwxyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbi7iwxyr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5bz89k9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5bz89k9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpggwxwwzq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpggwxwwzq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6lwagaod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lwagaod/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpup4bwyk_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpup4bwyk_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmwi9q_xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwi9q_xp/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ______________________ test_nearest[None-False-opposite] _______________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1508357 | 1508870 | a | 0 | - | E | chr1 | 1508357 | 1508870 | a | 0 | - | E | chr1 | 2035969 | 2036482 | a | 0 | - | E | chr1 | 1508357 | 1509641 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65538 | 72195 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY3QPb/vFauJxci9biu65EDZWkSIGBiZGIGBgZGZikBdkYLAQZ2FhY2ZkZWZgYWJgYGSESIIhmOBhUNK9KcXAwMvAwAAA8HcIgg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfyh1g2f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfyh1g2f5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ho5g6o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ho5g6o0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbrmfenja/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrmfenja/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchvj9nyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchvj9nyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpui25vq1v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpui25vq1v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp668388k6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp668388k6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2kh16nin/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kh16nin/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp45infya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp45infya/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7pojrngk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pojrngk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvtansj8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtansj8b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9t5o30e8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9t5o30e8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5o4_kcda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5o4_kcda/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdyx3dkjp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdyx3dkjp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpso4t9k6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpso4t9k6h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4vukxod3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4vukxod3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf29f7yih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf29f7yih/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd15ve21z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd15ve21z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3053yygq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3053yygq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp95u32ua1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95u32ua1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpalb3xx22/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalb3xx22/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_v5b1gem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_v5b1gem/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpya9m9y11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpya9m9y11/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0d14lo4x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0d14lo4x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpajy3qjze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpajy3qjze/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv44ixcfw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv44ixcfw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprt8mb_6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprt8mb_6r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ke8r90m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ke8r90m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp112h4d26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp112h4d26/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsbhaw_j_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbhaw_j_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdf1s8_ie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf1s8_ie/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9me4mwlq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9me4mwlq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfjh99jcf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjh99jcf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdcmxjkmu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcmxjkmu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjbvi3ukt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbvi3ukt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppbea88qq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbea88qq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1it1p9d4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1it1p9d4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqtrn80nj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqtrn80nj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6yz_w0ok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yz_w0ok/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppaqjjvbm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppaqjjvbm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfck033h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfck033h_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps36vl7r1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps36vl7r1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgzlpmoy0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzlpmoy0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7uh1mb27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7uh1mb27/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqeqtaj_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqeqtaj_e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4sghkxcm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4sghkxcm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi9zdu6uy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi9zdu6uy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx38351iz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx38351iz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbwr_zv5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbwr_zv5g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe14xr_zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe14xr_zc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp16uo26i6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp16uo26i6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ohrjrcq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ohrjrcq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnlt5zof5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlt5zof5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgzvhdmzj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzvhdmzj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw50skoc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw50skoc0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4g1dxxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4g1dxxc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjxd4qrs0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxd4qrs0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk0rypgwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0rypgwj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd_xzpdqf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_xzpdqf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvlvc7886/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvlvc7886/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5pgmdjzn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pgmdjzn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb0zi_oys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0zi_oys/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyesm_ec1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyesm_ec1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbuia1tmw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbuia1tmw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp809t6f_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp809t6f_8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzzfqlke2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzfqlke2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwrw1f_2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrw1f_2a/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain63-method_chain63] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 458767 | 459024 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65538 | 65539 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 154 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkYGdiEGdkYGBkZACSQMzIzsDHAGHz9DCwMoAAMyNMnoERABYvAOQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________________ test_k_nearest_1_vs_nearest __________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 @settings( > max_examples=max_examples, deadline=deadline, print_blob=True, suppress_health_check=HealthCheck.all()) tests/test_binary.py:576: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:583: in test_k_nearest_1_vs_nearest result_k = gr.k_nearest(gr2, k=1, strandedness=None, overlap=True, how=None) pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest_1_vs_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:24: ValueError ___________ test_three_in_a_row[strandedness_chain31-method_chain31] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr22 | 1146804 | 1146805 | a | 0 | + | E | chrY | 9758755 | 9762860 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr22 | 1146804 | 1150390 | a | 0 | + | E | chrY | 9758755 | 9762860 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 852764 | 853289 | a | 0 | - | E | chr1 | 852764 | 853289 | a | 0 | - | E | chr1 | 852764 | 853289 | a | 0 | - | E | chr22 | 852764 | 853289 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 42 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY0qRmtbEFmkS6c3AyMAgL8rMwMzIIM7AzSg45YUSQ+knoTOC9ZuZGK0N1QU42BgZkhiAgIkUPQx+fEBFDMys4X6MrMz5siysjMovmZiSqxatZZCXZmYQBZnIyMsszSDFxMPACAB58hgi') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________ test_nearest[upstream-True-False] _______________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 985345 | 985347 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1806 | 3343 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 65 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2Rj4PnJwAiEDAz8nGAKgsFCjCA2Oy+IyQZkMQAAMUoBSQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65537 | 68869 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 70 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2Rj4PnJwMDIycDIAAGMjEAmIyMThGZgYAZJsPOCKQAvmAE/') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 | (and 450 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0tneehwe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0tneehwe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvvihikvu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvvihikvu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7s7htvk7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7s7htvk7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3owzwpgk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3owzwpgk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvr5bw_kv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvr5bw_kv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfu8uig1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfu8uig1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzpyvajzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzpyvajzc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpszu_meeq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszu_meeq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdillexjk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdillexjk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprieilhl0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprieilhl0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyu5o2ylo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyu5o2ylo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0h3ht22e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0h3ht22e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiyal6agj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiyal6agj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0j12bh9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0j12bh9n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu42gkuon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu42gkuon/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1fk9086t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fk9086t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp32l2rlnu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32l2rlnu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgkzddrvg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgkzddrvg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvqmnewt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvqmnewt4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu68hnwgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu68hnwgj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprrh_4fni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrh_4fni/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp94ihzwmy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp94ihzwmy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp305qe_dm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp305qe_dm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp44gp77o3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44gp77o3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpei9kba81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpei9kba81/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb60ttppw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb60ttppw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph5p8rf3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5p8rf3l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8i5allf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8i5allf8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptmix5x6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptmix5x6i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpouopu2fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpouopu2fa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_j4lqadw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_j4lqadw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmi49nlrk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmi49nlrk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_hrprej5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_hrprej5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoe4bj87v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoe4bj87v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbnddpw3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbnddpw3i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn5o6tzjl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn5o6tzjl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwvci5l7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvci5l7y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbnm90pkb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbnm90pkb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4bycc89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4bycc89/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpehh862g5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehh862g5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprekdvr3z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprekdvr3z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaehbhwy5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaehbhwy5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphtf2s86l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtf2s86l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplyrylm2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplyrylm2h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi64lwuty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi64lwuty/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp2kltlkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2kltlkv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp39y1gy0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39y1gy0h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3bnw8xa8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bnw8xa8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5nkpnnt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5nkpnnt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpohawgd1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohawgd1d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3qk63o4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3qk63o4e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg8dmrmff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8dmrmff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbazm5eq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbazm5eq2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpumd8bbze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumd8bbze/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3gmkr6r0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3gmkr6r0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp47_x86_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47_x86_4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw6lgfyks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6lgfyks/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0zivstlg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0zivstlg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwm7o425s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwm7o425s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo2z1r086/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2z1r086/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkc7neo_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkc7neo_e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpww2c7d3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpww2c7d3l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm5lx99xg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5lx99xg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbei9sogj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbei9sogj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw1t87s74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1t87s74/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp__xpnbkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__xpnbkc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp45p0utob/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45p0utob/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjoi166qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjoi166qx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnfe93shx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfe93shx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqrj6l3ed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrj6l3ed/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbhrqcpd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhrqcpd3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdqpf_zpc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqpf_zpc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvrnebs80/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrnebs80/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvvu6wohk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvvu6wohk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt7ozys4l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7ozys4l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp458v025a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp458v025a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj6dafjga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj6dafjga/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain64-method_chain64] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain0-method_chain0] ____________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 244 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _______________________ test_nearest[upstream-True-same] _______________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 200450 | 200451 | a | 0 | + | | | chr1 | 200450 | 210231 | a | 0 | + | | | chr1 | 200450 | 207400 | a | 0 | + | | | chr1 | 200450 | 210100 | a | 0 | + | | | ... | ... | ... | ... | ... | ... | | | chr1 | 200450 | 200555 | a | 0 | + | | | chr1 | 131346 | 134689 | a | 0 | - | | | chr1 | 200450 | 210206 | a | 0 | - | | | chr1 | 200450 | 201779 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 131346 | 134689 | a | 0 | + | | | chr1 | 200450 | 203525 | a | 0 | + | | | chr1 | 200450 | 206629 | a | 0 | + | | | chr1 | 200450 | 200451 | a | 0 | - | | | ... | ... | ... | ... | ... | ... | | | chr1 | 200450 | 210206 | a | 0 | - | | | chr1 | 200450 | 203525 | a | 0 | - | | | chr1 | 200450 | 203525 | a | 0 | - | | | chr1 | 200450 | 210100 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 131 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXictc8/S8NAGAfg33vv5e6S3DXWilSTSlBScbCNKMQ/LX4FQXDoHlAX94K4FdTBQSguDm5uxUkcxMXJrbODX8PBwbq4OvkNnofKDpfe7tu4GA6fxby6SbTa76dnvDC6y8vLd6HS8wOx0xt/8dHebUUev9xvP32MPi/CQe9Ktk9xDcXQoBloQVWEHBFBu0ogapuvzVg4bq+66uMU9YGGM3LlpL7IUaiXs4dZv76mcWjFlvVTmTQ3rKXY5M4IOOlxN5TTga14hZcXWAq5q1rrnThDxMSCLMehaPAcSCtQ4JTnEaMVEdhxDZn1oazPDNBfxZ/YvxXNbxFIFCZFMnBmwvoGiZ5EQQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 126 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGBEoqBsAACRAAY=') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 471 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4s_nhcxn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4s_nhcxn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx4_v4qrs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx4_v4qrs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyk2wbz7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyk2wbz7i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9pwnye_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9pwnye_8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphthc_j_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphthc_j_q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 131346 134689 - 0 1 chr1 200450 200451 + 0 2 chr1 200450 200555 + 0 3 chr1 200450 201779 - 0 4 chr1 200450 206629 + 0 5 chr1 200450 207400 + 0 6 chr1 200450 210100 + 0 7 chr1 200450 210206 - 0 8 chr1 200450 210231 + 0 9 chr8 200450 204986 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 200450 | 200451 | a | 0 | ... | | chr1 | 200450 | 210231 | a | 0 | ... | | chr1 | 200450 | 207400 | a | 0 | ... | | chr1 | 200450 | 210100 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 200450 | 200555 | a | 0 | ... | | chr1 | 131346 | 134689 | a | 0 | ... | | chr1 | 200450 | 210206 | a | 0 | ... | | chr1 | 200450 | 201779 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 131346 134689 - 0 0 chr1 200450 200451 + 0 5 chr1 200450 200555 + 0 8 chr1 200450 201779 - 0 9 chr8 200450 204986 - 0 4 chr1 200450 206629 + 0 2 chr1 200450 207400 + 0 3 chr1 200450 210100 + 0 7 chr1 200450 210206 - 0 1 chr1 200450 210231 + 0 df2 Chromosome Start End Strand Distance 0 chr1 131346 134689 - 0 1 chr1 200450 200451 + 0 2 chr1 200450 200555 + 0 3 chr1 200450 201779 - 0 9 chr8 200450 204986 - 0 4 chr1 200450 206629 + 0 5 chr1 200450 207400 + 0 6 chr1 200450 210100 + 0 7 chr1 200450 210206 - 0 8 chr1 200450 210231 + 0 Actual Chromosome Start End Strand Distance 0 chr1 131346 134689 - 0 1 chr1 200450 200451 + 0 2 chr1 200450 200555 + 0 3 chr1 200450 201779 - 0 4 chr1 200450 206629 + 0 5 chr1 200450 207400 + 0 6 chr1 200450 210100 + 0 7 chr1 200450 210206 - 0 8 chr1 200450 210231 + 0 9 chr8 200450 204986 - 0 Expected Chromosome Start End Strand Distance 0 chr1 131346 134689 - 0 1 chr1 200450 200451 + 0 2 chr1 200450 200555 + 0 3 chr1 200450 201779 - 0 4 chr1 200450 206629 + 0 5 chr1 200450 207400 + 0 6 chr1 200450 210100 + 0 7 chr1 200450 210206 - 0 8 chr1 200450 210231 + 0 9 chr8 200450 204986 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjbrrflh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbrrflh2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxicq85bd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxicq85bd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 200450 200451 + 0 2 chr1 200450 200555 + 0 4 chr1 200450 206629 + 0 5 chr1 200450 207400 + 0 6 chr1 200450 210100 + 0 8 chr1 200450 210231 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 200450 | 200451 | a | 0 | ... | | chr1 | 200450 | 210231 | a | 0 | ... | | chr1 | 200450 | 207400 | a | 0 | ... | | chr1 | 200450 | 210100 | a | 0 | ... | | chr1 | 200450 | 206629 | a | 0 | ... | | chr1 | 200450 | 200555 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 200450 200451 + 0 5 chr1 200450 200555 + 0 4 chr1 200450 206629 + 0 2 chr1 200450 207400 + 0 3 chr1 200450 210100 + 0 1 chr1 200450 210231 + 0 df2 Chromosome Start End Strand Distance 1 chr1 200450 200451 + 0 2 chr1 200450 200555 + 0 4 chr1 200450 206629 + 0 5 chr1 200450 207400 + 0 6 chr1 200450 210100 + 0 8 chr1 200450 210231 + 0 Actual Chromosome Start End Strand Distance 0 chr1 200450 200451 + 0 1 chr1 200450 200555 + 0 2 chr1 200450 206629 + 0 3 chr1 200450 207400 + 0 4 chr1 200450 210100 + 0 5 chr1 200450 210231 + 0 Expected Chromosome Start End Strand Distance 0 chr1 200450 200451 + 0 1 chr1 200450 200555 + 0 2 chr1 200450 206629 + 0 3 chr1 200450 207400 + 0 4 chr1 200450 210100 + 0 5 chr1 200450 210231 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiqld2dd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqld2dd7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsqeupm_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqeupm_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2egw1cjp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2egw1cjp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7n46412q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7n46412q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe0ng_ijp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0ng_ijp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7345081 7352943 - 0 1 chr15 330069 334923 - 0 2 chr15 1266499 1272547 - 0 3 chr15 2284820 2293350 + 0 4 chr15 4183569 4191601 - 0 5 chr15 6442257 6443379 + 0 6 chr15 6535996 6540141 + 0 7 chr15 9186448 9192031 + 0 8 chr15 9525599 9525600 + 0 9 chr15 9525599 9529679 - 0 10 chr15 9525599 9535469 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7345081 | 7352943 | a | 0 | ... | | chr15 | 6535996 | 6540141 | a | 0 | ... | | chr15 | 6442257 | 6443379 | a | 0 | ... | | chr15 | 9186448 | 9192031 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr15 | 4183569 | 4191601 | a | 0 | ... | | chr15 | 9525599 | 9529679 | a | 0 | ... | | chr15 | 9525599 | 9535469 | a | 0 | ... | | chr15 | 330069 | 334923 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr15 330069 334923 - 0 6 chr15 1266499 1272547 - 0 4 chr15 2284820 2293350 + 0 7 chr15 4183569 4191601 - 0 2 chr15 6442257 6443379 + 0 1 chr15 6535996 6540141 + 0 0 chr1 7345081 7352943 - 0 3 chr15 9186448 9192031 + 0 5 chr15 9525599 9525600 + 0 8 chr15 9525599 9529679 - 0 9 chr15 9525599 9535469 - 0 df2 Chromosome Start End Strand Distance 1 chr15 330069 334923 - 0 2 chr15 1266499 1272547 - 0 3 chr15 2284820 2293350 + 0 4 chr15 4183569 4191601 - 0 5 chr15 6442257 6443379 + 0 6 chr15 6535996 6540141 + 0 0 chr1 7345081 7352943 - 0 7 chr15 9186448 9192031 + 0 8 chr15 9525599 9525600 + 0 9 chr15 9525599 9529679 - 0 10 chr15 9525599 9535469 - 0 Actual Chromosome Start End Strand Distance 0 chr1 7345081 7352943 - 0 1 chr15 330069 334923 - 0 2 chr15 1266499 1272547 - 0 3 chr15 2284820 2293350 + 0 4 chr15 4183569 4191601 - 0 5 chr15 6442257 6443379 + 0 6 chr15 6535996 6540141 + 0 7 chr15 9186448 9192031 + 0 8 chr15 9525599 9525600 + 0 9 chr15 9525599 9529679 - 0 10 chr15 9525599 9535469 - 0 Expected Chromosome Start End Strand Distance 0 chr1 7345081 7352943 - 0 1 chr15 330069 334923 - 0 2 chr15 1266499 1272547 - 0 3 chr15 2284820 2293350 + 0 4 chr15 4183569 4191601 - 0 5 chr15 6442257 6443379 + 0 6 chr15 6535996 6540141 + 0 7 chr15 9186448 9192031 + 0 8 chr15 9525599 9525600 + 0 9 chr15 9525599 9529679 - 0 10 chr15 9525599 9535469 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd8rg0smm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd8rg0smm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3vg_j4nx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vg_j4nx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5d4r5wrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5d4r5wrz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjwmdm7_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwmdm7_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vh07amk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vh07amk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphrnqgolr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphrnqgolr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2urd0xie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2urd0xie/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk7bny52j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7bny52j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1dzbrfmm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1dzbrfmm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgam4su8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgam4su8t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdi18qxu7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdi18qxu7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpottiuao0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpottiuao0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgcm4o8sa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgcm4o8sa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa3ua1wfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa3ua1wfi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprbkxun9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprbkxun9m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpykxj0wco/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpykxj0wco/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqvoyz4uf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvoyz4uf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkhzwg_sq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkhzwg_sq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3kb04osm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3kb04osm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb707qgkr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb707qgkr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnw9lhmwe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnw9lhmwe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuc5qcqip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuc5qcqip/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ag74yud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ag74yud/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfsxlk15u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfsxlk15u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi5ej3w3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5ej3w3_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu7uedeb_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu7uedeb_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb0njvgee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0njvgee/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1m963lm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1m963lm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpluac_oju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpluac_oju/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc3zsp7b2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3zsp7b2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqwbkp7f3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwbkp7f3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp802_pcie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp802_pcie/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyvonqn27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvonqn27/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpexo_aczo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpexo_aczo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcn062mew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcn062mew/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp7xk23j7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7xk23j7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx8rekof8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8rekof8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn63kwwfr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn63kwwfr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw5m6f5qb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5m6f5qb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptre1r4v_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptre1r4v_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpha_07k8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpha_07k8d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa8pgkwiw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8pgkwiw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xlux1wu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xlux1wu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdloxdpr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdloxdpr4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0fiag53a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fiag53a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptqi9rcv4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqi9rcv4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi4izknxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4izknxb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxh8cia0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxh8cia0o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfrqwpcpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfrqwpcpm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnin0olvp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnin0olvp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8plbynpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8plbynpk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmgwke8w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmgwke8w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd9a4opjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd9a4opjg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpop5y3xrs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpop5y3xrs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp38uwemg2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38uwemg2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps9ayvomj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9ayvomj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk7t5p25w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7t5p25w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0yzwg57g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0yzwg57g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpah8bqxoj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpah8bqxoj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp85nqiduq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85nqiduq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvf61ti6f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvf61ti6f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp4g7s674/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4g7s674/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgghihywt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgghihywt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptjxfp06q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptjxfp06q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptvimigmu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvimigmu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4290pp2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4290pp2s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbbsnxwtp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbsnxwtp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphbrz7kd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbrz7kd7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprl_sqvao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprl_sqvao/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8_xpv7qu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_xpv7qu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp06r7ydnp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06r7ydnp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ffq2pd8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ffq2pd8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyz16payw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyz16payw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp39kzedke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39kzedke/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6o5pyvvp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6o5pyvvp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1xcmcazs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1xcmcazs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1282 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3_tl3sle/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_tl3sle/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpujhdqw7_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujhdqw7_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptuui22i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuui22i1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphhcbmef1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphhcbmef1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp417k8f06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp417k8f06/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpihpjv1v2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihpjv1v2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpue93r96j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpue93r96j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphzvyeajx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphzvyeajx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaxntjglh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxntjglh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_l6fkzud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_l6fkzud/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp98i_ba47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98i_ba47/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp90o40soc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90o40soc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgfss6hzk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfss6hzk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwg2xkcfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwg2xkcfc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxwpsi2zg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwpsi2zg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpho1he1sr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpho1he1sr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaxhdsuq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxhdsuq5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb2ku8e0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb2ku8e0h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_yy3q1y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_yy3q1y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1lvs6izj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lvs6izj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpueq3vu2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpueq3vu2t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9t399ran/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9t399ran/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphvnc65fb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphvnc65fb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain33-method_chain33] ___________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain66-method_chain66] ___________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 327681 | 327939 | a | 0 | + | E | chr1 | 327681 | 327939 | a | 0 | - | E | chr1 | 327681 | 327939 | a | 0 | - | E | chr1 | 327681 | 327939 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr1 | 327681 | 327939 | a | 0 | - | E | chr1 | 327681 | 327939 | a | 0 | - | E | chr1 | 327681 | 327939 | a | 0 | - | E | chr1 | 327681 | 334606 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1250309 | 1251334 | a | 0 | - | E | chr1 | 1250309 | 1251334 | a | 0 | - | E | chr1 | 333573 | 334598 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 258 | 522 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY4zcw5RjfkiI1Y7JcCUrx9f+x1YMVWwZMzQD2Rl1WE2K2dnYWVmTWEOZXPVYNZhyvVhZGLh4WFkY2XgZ2BkYGIHQhJWBQYKTV5oHyGVk5OflANGJKq+UmYXN42TY2TizRZUY2JgYpRgZmZgZOYFaeJnkWMVZGBiERVgYWFjA2lgZGRmAgI0BxAMZy8gONhwAeyIQTQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 327681 | 329476 | a | 0 | ... | | chr1 | 327681 | 329757 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain68-method_chain68] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_nearest[upstream-True-opposite] _____________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 129 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4gU6BmQAApQAH') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 125 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGOGBkRBKCsgEApQAH') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 458 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz811fk0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz811fk0c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0w6p252o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0w6p252o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpantmcdwl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpantmcdwl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfz0zpu9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfz0zpu9w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxidh4sch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxidh4sch/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0hdr7sbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hdr7sbn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7doh4_7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7doh4_7x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprhmbcqmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhmbcqmh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp01w9wj9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01w9wj9i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt_u9b4o1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_u9b4o1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3w0fy712/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3w0fy712/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwrrrpf92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrrrpf92/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmo2uuddq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo2uuddq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ummbvgp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ummbvgp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfczj5n4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfczj5n4k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp16jdixi3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp16jdixi3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps15pq0xa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps15pq0xa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_9hy9_st/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_9hy9_st/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpubrwax_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpubrwax_q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvrzio4ke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrzio4ke/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2q9mdwml/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2q9mdwml/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptqcsnoet/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqcsnoet/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3bfv65sf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bfv65sf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsuprsf5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsuprsf5d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpipvwoc6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipvwoc6m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf91yqx5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf91yqx5h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbnwhhgnn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbnwhhgnn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeo7o4w_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeo7o4w_2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgktj_24c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgktj_24c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprhh4bl7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhh4bl7t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5gvezy7j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gvezy7j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvj34s39m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvj34s39m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp__ey4ugr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__ey4ugr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5fgamy71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fgamy71/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpex70led7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpex70led7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx994d2c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx994d2c9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7vknj1v4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vknj1v4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8nmik51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8nmik51/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsbjacfu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbjacfu3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptcghb2sa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptcghb2sa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmu7y4krg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmu7y4krg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe17mwe2y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe17mwe2y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu1s5a_gm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu1s5a_gm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpck09kkea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpck09kkea/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpodhs52k5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodhs52k5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpocryu6jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpocryu6jl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp82v4sp6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82v4sp6p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptr2gjkvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptr2gjkvm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8u55e1fz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8u55e1fz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsdp55lip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsdp55lip/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpct2zl8y5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpct2zl8y5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe3hot0it/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe3hot0it/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpipxdlgxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipxdlgxl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7n2al21a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7n2al21a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzzhgc4_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzhgc4_e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplb7gcdsy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplb7gcdsy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjrtg9ofp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjrtg9ofp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7au3acw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7au3acw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprd87k58h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprd87k58h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjzjnqlax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzjnqlax/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mtfdbke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mtfdbke/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpngj6ui7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpngj6ui7e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw2j0_ngc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw2j0_ngc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuij0gx9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuij0gx9_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt7if8_bw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7if8_bw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3kprbkta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3kprbkta/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmn8bzdwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmn8bzdwk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5uncuhd1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5uncuhd1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd1wlc9cf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd1wlc9cf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkm_u4qg2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkm_u4qg2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa7494mcm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7494mcm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5dfabvxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5dfabvxg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxmmao26k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmmao26k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_545kb12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_545kb12/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ikbwflg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ikbwflg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptb6_db2u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptb6_db2u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp265bpjl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp265bpjl6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgs4sybu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgs4sybu3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp57jynilu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57jynilu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpomzxr7sv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomzxr7sv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3bio8rkj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bio8rkj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7r3u3jni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7r3u3jni/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2m_i2po6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2m_i2po6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1282 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpod255t9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpod255t9c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gtgddg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gtgddg5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp07dxjxyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07dxjxyr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcb7khgub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcb7khgub/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9in8kou6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9in8kou6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8l7uxj9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8l7uxj9r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnx5j53nb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnx5j53nb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_1f14jyi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1f14jyi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu41p33fc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu41p33fc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8znmec12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8znmec12/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_m30auhj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_m30auhj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnmnbwe8m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmnbwe8m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa12aalzm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa12aalzm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprw49u6se/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprw49u6se/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq8gh8y6c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq8gh8y6c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg3hwn_36/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3hwn_36/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppwsfv7c1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwsfv7c1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8t1y8fhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8t1y8fhy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxq1wai__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxq1wai__/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplog49o73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplog49o73/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz5q1t7nh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5q1t7nh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxs04wr4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxs04wr4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpihxl99s7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihxl99s7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphm4gvesn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphm4gvesn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqqkyu350/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqkyu350/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvcv2__q6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcv2__q6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72bj4vly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72bj4vly/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93u2f56i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93u2f56i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwm2yiqgh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwm2yiqgh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm7ju84zu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7ju84zu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5mm1173/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5mm1173/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4m6xeyeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4m6xeyeh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvirunjwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvirunjwm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptzb5iqb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzb5iqb6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpomj_t8v9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomj_t8v9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdwnu_l81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwnu_l81/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpktn9dg3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktn9dg3d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpftsk8jby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpftsk8jby/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu2f5kz90/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2f5kz90/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_6rsh5b5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6rsh5b5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptj7c9hmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj7c9hmb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0uwd580a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0uwd580a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg8hsn7uz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8hsn7uz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpck2tjlil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpck2tjlil/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdhy_qdkp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhy_qdkp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpryfj_our/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpryfj_our/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9uus7hzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9uus7hzz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoy5r0iec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoy5r0iec/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpog2fuf4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpog2fuf4p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7v6m4ztl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7v6m4ztl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxeft3fxi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxeft3fxi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain157-method_chain157] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain115-method_chain115] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 1794 | a | 0 | + | E | chr1 | 1755546 | 1764871 | a | 0 | + | E | chr1 | 9959246 | 9961039 | a | 0 | + | E | chr1 | 1268007 | 1269800 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr1 | 1268007 | 1269800 | a | 0 | + | E | chr1 | 1268007 | 1269800 | a | 0 | + | E | chr1 | 1268007 | 1275956 | a | 0 | + | E | chr1 | 1268007 | 1271357 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 259 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 460289 | 460290 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 394241 | 394554 | a | 0 | + | E | chr1 | 69126 | 70412 | a | 0 | + | E | chr1 | 262408 | 262721 | a | 0 | + | E | chr1 | 460038 | 462867 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYxKVN05nrJ8xrY6dqZqBgYG1ojm4kMnlQuqTWIZLrCm378j80f9b03eROeSjVe5208L7n2rENXlYdQQd/Zk4Ll1O/9b8NeluHoMyDx8LAyMDoyQfPzcnU+i/f1rTv/uK8fMxZix8fvRHhuuG6z+kTs5U5GJUYADZYsbDy8QgeFLgxVtNPeFINVX2XN3f8jyWfJwcoTqxvKLM7CyM5aY/VXIU+XgZGQzNN7EDzQYidgZukBNBLmOJhriMLRDoMiZ8LmNjBbqLmZ1VjJ2NQYOVQRxoECMjF9A8ZqBZDMxMsmxczKrngDZxMjIxabDxsIJcxsDBCPINEys7KyszIw8jH5ACOoqdlRHoTTYWBgYpJktuHm5GVlZWBiZGCwkmRlagwxiArhUEGgsALAdMOg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3522 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain70-method_chain70] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 8596991 | 8597110 | a | 0 | + | | | chr1 | 30466 | 34543 | a | 0 | - | | | chr1 | 9468681 | 9470018 | a | 0 | - | | | chr1 | 10000000 | 10007054 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 919140 | 924267 | a | 0 | - | | | chr1 | 524290 | 529413 | a | 0 | - | | | chr1 | 7939 | 8965 | a | 0 | - | | | chr1 | 1311289 | 1314107 | a | 0 | - | | | ... | ... | ... | ... | ... | ... | | | chr1 | 11533 | 17935 | a | 0 | - | | | chr1 | 11533 | 14351 | a | 0 | - | | | chr1 | 11533 | 14351 | a | 0 | - | | | chr1 | 11533 | 14351 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr8 | 3598094 | 3600657 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 167 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicJY6vS0NhGEaf5313v/vdXxvC1bntzquIOJALE1TGsBjEJgiCiJjEuGCZQcRgFkRBLAbDokaDzSCYTFabMAQN/gPiB9Zz4HCM3rwG7Z81ju0ub5r+xe0ON162i8vyB3KfFfRwSCsHg+/3p0F2fmQrrJ4Wv5keX1+dIECr8pXIVrEw9+h1RmC11zhLETBBH006zxIDNFhTloTg9Nvw/m72+XNlfWmYaCStUEY1j8VnVve6Op9IFGmurSTyFfQeFBn2vbTbzmDJccYMhKRlqEDsgnXxkYuDKql0rIYMLdgUQ4vJstmDjyKeMqhRTVlQ4oRY5qkoCSzOpAaIXEZYdUGHfCRY/d9DBLcHx/EHyo8qdA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 | (and 219 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2AQUGGAAkYGTAAABigANg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________ test_nearest[upstream-False-False] ______________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:115 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0ZGBgSAcZDFAADEAAc=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:118 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkgwesr9q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkgwesr9q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9wuffo1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9wuffo1n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm387jjwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm387jjwk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcfw5ramc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcfw5ramc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpukeco7xe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukeco7xe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpikrykxga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpikrykxga/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpndgnt_ha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndgnt_ha/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_m789ons/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_m789ons/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc1deoi4f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1deoi4f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4yiuw36b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yiuw36b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv_b2yf9o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_b2yf9o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkydjxfxi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkydjxfxi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9yu2rxc1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yu2rxc1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk3fl6hf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3fl6hf1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2f_idrww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f_idrww/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp58spz09_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58spz09_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp27rk_r25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp27rk_r25/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuhr8mnzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuhr8mnzw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6sso0ve6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sso0ve6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptfq6fw69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfq6fw69/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph6vjjosh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6vjjosh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvjy0ucx_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvjy0ucx_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfe8t6dkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfe8t6dkv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpddk2h2lt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpddk2h2lt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1cx4_91y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1cx4_91y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_miov0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_miov0u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5uqr1k25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5uqr1k25/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp920cyuht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp920cyuht/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj6wikr94/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj6wikr94/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjev0d6bg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjev0d6bg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyq1xpm81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyq1xpm81/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprlskuyh1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprlskuyh1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptdmi6xg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdmi6xg1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgxfpa6v6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgxfpa6v6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4yil6ack/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yil6ack/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpncgpu0j2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncgpu0j2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpheeex84p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpheeex84p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5u368n7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5u368n7w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoc6yo4iw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoc6yo4iw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1wzqm4z0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wzqm4z0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmwm92tbh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwm92tbh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj0k7akui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0k7akui/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp13xgudp5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp13xgudp5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbbipy4pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbipy4pf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe6z41bi_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6z41bi_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuexgfulm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuexgfulm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzxrn5kjs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxrn5kjs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_d8t_6ex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_d8t_6ex/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzarr_u2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzarr_u2w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfe_6pe5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfe_6pe5q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiafqw6aw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiafqw6aw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1pj352ki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1pj352ki/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbx62sdyf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbx62sdyf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmitnjta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmitnjta/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfquo404f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfquo404f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmthjwxga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmthjwxga/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpipuqy1s2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipuqy1s2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpocifia54/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpocifia54/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf_4s4m5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_4s4m5n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplkxn7dqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplkxn7dqh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2sd5pap4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2sd5pap4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6wkpt_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6wkpt_j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkz8nsc8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkz8nsc8p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv5r73627/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5r73627/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr1eo24pv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1eo24pv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfa83cek6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfa83cek6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy_jfha_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_jfha_g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplf7_c2ps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplf7_c2ps/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7h4dsi0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7h4dsi0a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpotn6skm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpotn6skm2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9goyuxui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9goyuxui/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprxc5diqn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxc5diqn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8c7rgxpf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8c7rgxpf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp481drvej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp481drvej/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqdji3_g_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdji3_g_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppz64h5gt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppz64h5gt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptti8nmpf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptti8nmpf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphzo9cw71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphzo9cw71/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuyy6_k5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyy6_k5l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx0ilw03a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0ilw03a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnuyfv_l8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnuyfv_l8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy77ln5co/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy77ln5co/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0lrbw9v3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0lrbw9v3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplobcyeay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplobcyeay/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqu7ms2aa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqu7ms2aa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_8t46lc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_8t46lc5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpirdphlhb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpirdphlhb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo6qyv7bg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6qyv7bg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb0vg_05u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0vg_05u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4j827vm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4j827vm_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpieemmoka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpieemmoka/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeu3rb0b2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeu3rb0b2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnonacz5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnonacz5q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbmo14ni7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmo14ni7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa2pcng7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2pcng7a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmvyuazfv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvyuazfv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_3ltzi59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3ltzi59/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36jvgovr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36jvgovr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnukh0rf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnukh0rf1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw3sm_5iy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3sm_5iy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplrodcw2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplrodcw2s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwirhmjdl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwirhmjdl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb5_mxusc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5_mxusc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2gf9h8xt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gf9h8xt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsoa1vu96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsoa1vu96/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwohqlmvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwohqlmvz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprrqqn4ey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrqqn4ey/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp71vbhgv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp71vbhgv6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyigvkk7u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyigvkk7u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0lidrmdl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0lidrmdl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmvds7hgx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvds7hgx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpumanjbz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumanjbz3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsxvfao5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxvfao5e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk2_tievm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2_tievm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqta_twc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqta_twc8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv69oa7f0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv69oa7f0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8x423gz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8x423gz4/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain158-method_chain158] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain117-method_chain117] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain159-method_chain159] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ______________________ test_nearest[upstream-False-same] _______________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65538 | 65539 | a | 0 | - | | | chr1 | 65538 | 65539 | a | 0 | - | | | chr1 | 65538 | 65539 | a | 0 | - | | | chr1 | 65538 | 65539 | a | 0 | - | | | ... | ... | ... | ... | ... | ... | | | chr1 | 597264 | 597265 | a | 0 | - | | | chr1 | 65538 | 65539 | a | 0 | - | | | chr1 | 65538 | 65539 | a | 0 | - | | | chr1 | 65538 | 65539 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 9 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 721163 | 727052 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 105 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY4wv3X2JsWbGtHpG5aoj5Ywcbb+cGK2nWOcxJnl5qzFKMzAwMPIyMLAysjOa8ADZjKzsnLL8jKwMUowMjAz8IGkgxQfigCE3IxeQKhQHSQAAgsMMeA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz68peloo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz68peloo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxkltu9p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxkltu9p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmmay8v6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmay8v6e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp34gn4ehl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34gn4ehl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9sz2u_qj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9sz2u_qj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp138im99l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp138im99l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ttw6zj7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ttw6zj7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpye7zpdur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpye7zpdur/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt2ufsto2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2ufsto2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe5_10kxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5_10kxv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ngkbj_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ngkbj_e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp06mti84s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06mti84s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyyrkwtp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyyrkwtp8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptpvyh7qa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpvyh7qa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptuj67stu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuj67stu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdxqojjnp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxqojjnp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvr5cva4w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvr5cva4w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_agjhdh8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_agjhdh8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp3v5f1y7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp3v5f1y7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9l7upd4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9l7upd4s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzc0ruiiz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzc0ruiiz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmputmxweqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputmxweqo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_6nda80s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6nda80s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgm_e0r87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgm_e0r87/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpayhvwyqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpayhvwyqh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpio8asjx4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpio8asjx4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmo8kogf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo8kogf1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvxgroubv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvxgroubv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn7yjkzas/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7yjkzas/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzajj47fj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzajj47fj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu9zedqlw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu9zedqlw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpty63mhld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpty63mhld/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpck31k23w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpck31k23w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu317t3xn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu317t3xn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc2stqqr2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2stqqr2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2zs3oo5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zs3oo5m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcsl086i3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcsl086i3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1guncl2x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1guncl2x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprg2etp3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprg2etp3x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_fv5vh6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fv5vh6d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxd8z0mgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxd8z0mgf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdzhzf9gi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzhzf9gi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf8gi3ts1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8gi3ts1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9x3ejomv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9x3ejomv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphwalk4b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwalk4b3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8v1y64ii/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8v1y64ii/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphns7zckc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphns7zckc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6r9bsjl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6r9bsjl9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi412axy9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi412axy9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps__gpzgx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps__gpzgx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp43uywx6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43uywx6q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd4i9km2o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd4i9km2o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp89aq1cqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89aq1cqg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuqatldqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqatldqt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprple9p7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprple9p7m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp152c1qf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp152c1qf9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizspav3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizspav3p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3337z6hq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3337z6hq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaaruydp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaaruydp4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5zyenlna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5zyenlna/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq853zaya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq853zaya/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqqwzn_jh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqwzn_jh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvk9mixlz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvk9mixlz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5glvvuv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5glvvuv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptyg51f86/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptyg51f86/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3hikes00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3hikes00/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppbmta1h9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbmta1h9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo2luc21y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2luc21y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps1zcdm2g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1zcdm2g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpreidy0sa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpreidy0sa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4bi84lr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4bi84lr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphbwnjmqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbwnjmqy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxc3nb6cj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxc3nb6cj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprckzzc58/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprckzzc58/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpelqdy7rq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpelqdy7rq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpotvp_p84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpotvp_p84/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc7rk0nkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc7rk0nkc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5_zl39va/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_zl39va/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_gmm833z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gmm833z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjimc57r_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjimc57r_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphj_46wlc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphj_46wlc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1rhai3dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rhai3dk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2c6_f5gp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2c6_f5gp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuxhnd5rb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuxhnd5rb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppykr0j40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppykr0j40/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbnner12w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbnner12w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4n520409/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4n520409/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi7cuzp63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7cuzp63/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprrh5hotn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrh5hotn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjfcx8dui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfcx8dui/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptkqt4hw8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkqt4hw8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpljvvxxts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpljvvxxts/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpto906mei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto906mei/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiw3fzenr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiw3fzenr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9j69gnvu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9j69gnvu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyjq71ffu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyjq71ffu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpujhfkcuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujhfkcuo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdwttmq82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwttmq82/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_zgma633/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_zgma633/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpajs7ir2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpajs7ir2t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3b7_plrt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3b7_plrt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnllglusz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnllglusz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2nbj191f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2nbj191f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvk5lvswc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvk5lvswc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfku9kwbo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfku9kwbo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6jzaze7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6jzaze7q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfdtsde9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdtsde9s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ofekl44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ofekl44/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeqv5ivqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqv5ivqt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplo74jrts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplo74jrts/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxy8rqsbq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxy8rqsbq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7w4800ze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7w4800ze/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsm3_zd74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsm3_zd74/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfb1lwj38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfb1lwj38/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaxj4s7rd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxj4s7rd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk2gzaw1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2gzaw1c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfzaapstu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzaapstu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1rhpnxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1rhpnxr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbuw24zpu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbuw24zpu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp_73c0ay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_73c0ay/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv604dkcr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv604dkcr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp81er3gpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81er3gpz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8jiv4ujw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jiv4ujw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3t86xr4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3t86xr4a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpww7z96tb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpww7z96tb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnd8ho37g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnd8ho37g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfmi00e57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfmi00e57/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbe2mm0h9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbe2mm0h9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpva8w26yf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpva8w26yf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxgli4kkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgli4kkw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy6kj_6tm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6kj_6tm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpid8wpt0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpid8wpt0c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd_8ah6so/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_8ah6so/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmup157i3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmup157i3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuwdxzi5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwdxzi5d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpljtl3c3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpljtl3c3n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2p0qj8ro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2p0qj8ro/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp94dpl8r8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp94dpl8r8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbsx2mqvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbsx2mqvx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ufgj_6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ufgj_6p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqzq_lgf4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzq_lgf4/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain71-method_chain71] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4gU6hcQAA6QAH') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 | (and 77 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BAAEZMCgAAQwAE') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 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('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain160-method_chain160] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges 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('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain119-method_chain119] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 4827105 | 4836700 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 66055 | 66340 | a | 0 | + | | | chr1 | 728579 | 728864 | a | 0 | - | | | chrX | 1117441 | 1117699 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr19 | 514 | 8195 | a | 0 | - | | | chr19 | 228915 | 234042 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 167 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2cO8PzEwMDMwMjAwSC+x/W45/IHDLwM0qpVDFxAMVbR19PLTy58stxLfP2Ej3vk1b847Vt372LN1hB2Bp5jtQVKOVZwBiPQGBYGHkYGMQYGBiZGEUFeoJEM3HJMDOyMTGyMIMAgwyjDBDSWgVWeS4KRnYH7lgyjNHM1UL0QUJK5zoiflZGVkYtBBKifgZ+DkdVAW4SNmZGfkcFNjoEBaAYLUDMAsLselw==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 | (and 368 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________ test_nearest[upstream-False-opposite] _____________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGOGBkxBBiAAAAngAG') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbydqhzzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbydqhzzi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4qft2c79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4qft2c79/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmtnzxvrf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmtnzxvrf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi045n2qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi045n2qh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiah43z_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiah43z_6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfl7k180t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfl7k180t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwpjetd00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpjetd00/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyle_90s_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyle_90s_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpze5idqz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpze5idqz5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprkcivx61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkcivx61/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4p6foy99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4p6foy99/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpznck3qno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpznck3qno/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9pakrv8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9pakrv8s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt3fe0036/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt3fe0036/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq_ygqo87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_ygqo87/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp37qsyyz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37qsyyz1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfy3uvhx_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfy3uvhx_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_4tg6ftz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4tg6ftz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6wr46504/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wr46504/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_9ge157k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_9ge157k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxp4heqo6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxp4heqo6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzf0c0i6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzf0c0i6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv3n3hr13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3n3hr13/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuisk6e9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuisk6e9k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpertojng3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpertojng3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyb6nb00i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyb6nb00i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnk6ewxg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnk6ewxg4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnhaybfcc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhaybfcc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp54mebc_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54mebc_e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdrt8zxof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrt8zxof/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuvdsbp6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuvdsbp6r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp11xzbm0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11xzbm0v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp66bp1pv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66bp1pv5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb5drvk1v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5drvk1v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnaj1ee7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnaj1ee7q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdx_5bniw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdx_5bniw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_wbe6g99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_wbe6g99/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_oggxo_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_oggxo_i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuchmdicp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuchmdicp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuvg69ohb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuvg69ohb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqg4hojs0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqg4hojs0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvap4cd6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvap4cd6t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6yzoauyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yzoauyq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcvpj3_to/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvpj3_to/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsac34sau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsac34sau/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbkqpocb1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkqpocb1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_epvjxsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_epvjxsm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpryq4p3c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpryq4p3c3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjnljmkpj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjnljmkpj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo7fml1k9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7fml1k9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwbsgzgng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwbsgzgng/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk8yvm8j8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8yvm8j8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7vl7nsdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vl7nsdq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprwuqdk9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprwuqdk9l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzxsgqry4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxsgqry4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm_azzng4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_azzng4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptmani3e1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptmani3e1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6rg31cz9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6rg31cz9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptk9_ov3g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptk9_ov3g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8dvn00ic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dvn00ic/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn8vpswvy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8vpswvy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfpikq89l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfpikq89l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzciice14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzciice14/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt_cs4fl2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_cs4fl2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1pnal_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1pnal_o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzdh6ezcy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzdh6ezcy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphgj14vox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgj14vox/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcz3np9ut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcz3np9ut/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxog1kpp7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxog1kpp7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2rzx61kw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2rzx61kw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv2n4k8uf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2n4k8uf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4_0z7hf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4_0z7hf1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp392jbnvn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp392jbnvn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5s64zu48/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5s64zu48/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppt4cgq7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppt4cgq7r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm044fje2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm044fje2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy1i0mdf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy1i0mdf6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf762jv7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf762jv7y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyc4xo3bd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyc4xo3bd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc9mivpto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9mivpto/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvo8wigl4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvo8wigl4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpccz0qscb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccz0qscb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ivnjpee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ivnjpee/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpetjn2cxe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetjn2cxe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1axjin30/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1axjin30/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp27vgb34y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp27vgb34y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpygpom4pc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygpom4pc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe5r9z65l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5r9z65l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdvea_t4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdvea_t4_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm9b_3d6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9b_3d6_/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain72-method_chain72] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65537 | 65541 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 1542 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:110 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicHYpBDgAwCMLKMGb/f7FoL5SAURefIFocVooNj4oRU6LNDvuUTgcKhgBG') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain161-method_chain161] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7752 | 7759 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 26898 | 26900 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 251 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgURV4v85B7QYjIwPb1NUMDIxAKOfO4MPAxgAVYgRDNoZMQQYGXhAbAPPIBvA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_nearest[downstream-True-False] ______________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 173322 | 180738 | a | 0 | - | | | chr1 | 173322 | 178804 | a | 0 | - | | | chr6 | 173322 | 182059 | a | 0 | - | | | chr11 | 173322 | 175128 | a | 0 | - | | | chr11 | 173322 | 180335 | a | 0 | - | | | chr21 | 173322 | 181577 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 655391 | 664721 | a | 0 | + | | | chr1 | 1181032 | 1190362 | a | 0 | + | | | chr1 | 555777 | 560684 | a | 0 | - | | | chr1 | 1181032 | 1190362 | a | 0 | - | | | ... | ... | ... | ... | ... | ... | | | chr16 | 1181032 | 1183389 | a | 0 | - | | | chr22 | 1181032 | 1190362 | a | 0 | + | | | chr22 | 1181032 | 1189240 | a | 0 | + | | | chrY | 1181032 | 1185771 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 69 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'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') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 901216 | 901473 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 64 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGBkrV7RDxQBisXzHohnZPABywIANJ8Dlg==') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 | (and 455 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8nzvuy7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8nzvuy7t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvwkvrm2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwkvrm2h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0q0bqp_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0q0bqp_6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_im0gtn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_im0gtn3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpphug7mqw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpphug7mqw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6v54b3m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6v54b3m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe89a9zwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe89a9zwn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpexcbsn27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpexcbsn27/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzxr3ppg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxr3ppg1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppxviy25g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxviy25g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6gol555z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6gol555z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppbfsabms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbfsabms/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptmi2atz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptmi2atz4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0bu6lut0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0bu6lut0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptuaz_ya4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuaz_ya4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7wptm6w8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7wptm6w8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo8iw565x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo8iw565x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwq6uu_h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwq6uu_h_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeh3pmo8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeh3pmo8_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph3kh0njb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3kh0njb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppsn_7xsj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppsn_7xsj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuobhh08d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuobhh08d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm9vld_vz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9vld_vz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqa63_4ug/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqa63_4ug/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmdmr691x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmdmr691x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpymkhno87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymkhno87/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprkj58227/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkj58227/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_i91jm_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i91jm_j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0kzj0i5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kzj0i5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfbxtzhmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfbxtzhmz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplncozkwp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplncozkwp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7o4mcnwu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7o4mcnwu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6t61hta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6t61hta/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptwxbpmcd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptwxbpmcd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvnz_nb4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvnz_nb4y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_8he5q0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_8he5q0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6nnj4j6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6nnj4j6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbce4rt5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbce4rt5a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwwbxuh8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwbxuh8d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpycm92_xc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpycm92_xc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4yi85e0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yi85e0m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplhd2oik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplhd2oik/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfl729lau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfl729lau/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7838 + 0 1 chr1 1 7838 + 0 2 chr1 1 7838 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7838 | a | 0 | ... | | chr1 | 1 | 7838 | a | 0 | ... | | chr1 | 1 | 7838 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7838 + 0 1 chr1 1 7838 + 0 2 chr1 1 7838 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 7838 + 0 1 chr1 1 7838 + 0 2 chr1 1 7838 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7838 + 0 1 chr1 1 7838 + 0 2 chr1 1 7838 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7838 + 0 1 chr1 1 7838 + 0 2 chr1 1 7838 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp09_s4b22/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp09_s4b22/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr4w4p2gb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr4w4p2gb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfkcyb0g_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkcyb0g_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl9tp_yax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9tp_yax/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2xba3f7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2xba3f7c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93h9375m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93h9375m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu0ndjhyg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0ndjhyg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2v9b57ae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2v9b57ae/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoigxpmpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoigxpmpi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoq5ohvt5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoq5ohvt5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbgm7rj4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgm7rj4o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpel25atod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpel25atod/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0f39o6_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0f39o6_i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfob38t19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfob38t19/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiz1ftklg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiz1ftklg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp08blgmc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08blgmc6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptchl9m7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptchl9m7q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo4gt2g7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4gt2g7i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcq5pmu9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcq5pmu9j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp279hmw5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp279hmw5b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa7bt43xt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7bt43xt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfx2a84e5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfx2a84e5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv2neoxpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2neoxpe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl5okp6hn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl5okp6hn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw7gsqali/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7gsqali/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt66fa8xq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt66fa8xq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvn48887w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvn48887w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12q66887/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12q66887/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpig6fnhjd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpig6fnhjd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps8p_5plb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8p_5plb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpppu6isv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpppu6isv6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeb72u093/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeb72u093/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpilacmze5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpilacmze5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1l8i947/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1l8i947/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwwfhmxa8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwfhmxa8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplgr1d8da/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgr1d8da/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd71ei79b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd71ei79b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe90twidh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe90twidh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain73-method_chain73] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2TgYwACRjjBwAihoDx0JgMAA6MAFg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr14 | 7796375 | 7798016 | a | 0 | ... | | chr21 | 7796375 | 7800090 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 18 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr14 | 7796375 | 7798016 | a | 0 | ... | | chr21 | 7796375 | 7800090 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 18 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain120-method_chain120] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2268323 | 2269869 | a | 0 | - | | | chr1 | 9870491 | 9878158 | a | 0 | - | | | chr21 | 2834056 | 2839097 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1089949 | 1099025 | a | 0 | - | | | chr18 | 6369544 | 6370378 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2340070 | 2343336 | a | 0 | + | | | chr1 | 2340070 | 2348696 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 182 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAUqgGhqBEBt4zEGGZSs/wARAgEdAwMAABQCAQEAAQBNKz6HCwFXIpyiAgIUoZJ+lpyaABoBcgYJFgAPE7AfBXgd8hEDAAEUABQAEQMACAEBEQEYAAABBAxPhDECLycbkAACAAAcEQIBAQAHAGVhMQcNAA8CAA0BRePvghChnAANADw0DgNBCQErI3MAAQEBBQABAAcAJEp6agJnHNI2AAEBAQQBAgABAA8PDwoDI7TlCgEmNYYhsQgBAwEEAAwMwQALAAAAAQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 | (and 78 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain162-method_chain162] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7 | 9 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr7 | 131329 | 138757 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkYwACHgYGZhDBwM3AyABCbEA+IwMjhAPiMjKBGLLMDAwACdEAZw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________ test_nearest[downstream-True-same] ______________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2241578 | 2241590 | a | 0 | + | | | chr1 | 2241578 | 2242737 | a | 0 | - | | | chr1 | 7169399 | 7169411 | a | 0 | - | | | chr5 | 9132386 | 9133385 | a | 0 | - | | | chr7 | 2241578 | 2241590 | a | 0 | + | | | chr15 | 9667924 | 9667936 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2148385 | 2149128 | a | 0 | - | | | chr2 | 6992044 | 6994419 | a | 0 | + | | | chr2 | 6119924 | 6122438 | a | 0 | - | | | chr4 | 7856106 | 7856107 | a | 0 | + | | | chr11 | 3151254 | 3153629 | a | 0 | - | | | chr16 | 2952 | 4755 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 5 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 128 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'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') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 257 | 258 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 126 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYzRuTbRggABGVBrGBQEAMJ8BVg==') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 472 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbs07h2py/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbs07h2py/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpogidcmdy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogidcmdy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp24gpkxy_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24gpkxy_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuh87v32i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuh87v32i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe5yxx0dz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5yxx0dz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw7i1ni2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7i1ni2f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvir9hn88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvir9hn88/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt2co7ixw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2co7ixw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 13061 13831 + 0 1 chr1 16142 16912 + 0 2 chr1 16142 16912 + 0 3 chr1 16142 16912 + 0 4 chr1 16142 22289 + 0 5 chr1 19457 20227 + 0 6 chr1 3801948 3802718 + 0 7 chr12 16142 16912 + 0 8 chr15 16142 16912 + 0 9 chr7 16142 16912 + 0 10 chr9 16142 16912 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 16142 | 22289 | a | 0 | ... | | chr1 | 16142 | 16912 | a | 0 | ... | | chr1 | 19457 | 20227 | a | 0 | ... | | chr1 | 16142 | 16912 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr7 | 16142 | 16912 | a | 0 | ... | | chr9 | 16142 | 16912 | a | 0 | ... | | chr12 | 16142 | 16912 | a | 0 | ... | | chr15 | 16142 | 16912 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 13061 13831 + 0 1 chr1 16142 16912 + 0 3 chr1 16142 16912 + 0 6 chr1 16142 16912 + 0 7 chr7 16142 16912 + 0 8 chr9 16142 16912 + 0 9 chr12 16142 16912 + 0 10 chr15 16142 16912 + 0 0 chr1 16142 22289 + 0 2 chr1 19457 20227 + 0 5 chr1 3801948 3802718 + 0 df2 Chromosome Start End Strand Distance 0 chr1 13061 13831 + 0 1 chr1 16142 16912 + 0 2 chr1 16142 16912 + 0 3 chr1 16142 16912 + 0 7 chr12 16142 16912 + 0 8 chr15 16142 16912 + 0 9 chr7 16142 16912 + 0 10 chr9 16142 16912 + 0 4 chr1 16142 22289 + 0 5 chr1 19457 20227 + 0 6 chr1 3801948 3802718 + 0 Actual Chromosome Start End Strand Distance 0 chr1 13061 13831 + 0 1 chr1 16142 16912 + 0 2 chr1 16142 16912 + 0 3 chr1 16142 16912 + 0 4 chr1 16142 22289 + 0 5 chr1 19457 20227 + 0 6 chr1 3801948 3802718 + 0 7 chr12 16142 16912 + 0 8 chr15 16142 16912 + 0 9 chr7 16142 16912 + 0 10 chr9 16142 16912 + 0 Expected Chromosome Start End Strand Distance 0 chr1 13061 13831 + 0 1 chr1 16142 16912 + 0 2 chr1 16142 16912 + 0 3 chr1 16142 16912 + 0 4 chr1 16142 22289 + 0 5 chr1 19457 20227 + 0 6 chr1 3801948 3802718 + 0 7 chr12 16142 16912 + 0 8 chr15 16142 16912 + 0 9 chr7 16142 16912 + 0 10 chr9 16142 16912 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwsl332m6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsl332m6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp22ktrswt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp22ktrswt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe6yoqkoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6yoqkoh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplho_xk37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplho_xk37/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu2t006o8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2t006o8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5xwylugh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5xwylugh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpib1oofna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpib1oofna/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpab7tg84f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpab7tg84f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzif10yoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzif10yoy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr3_qhjjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3_qhjjo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_enw2l7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_enw2l7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq0puuv5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq0puuv5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6k6heodk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6k6heodk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmwm011bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwm011bo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxkhvdwq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxkhvdwq5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvex5kbkn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvex5kbkn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo_kvzqu_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_kvzqu_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpssdfqefl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssdfqefl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9u40r2mh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9u40r2mh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdo5bgkvs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdo5bgkvs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp59drkz6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59drkz6v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2bs71qwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2bs71qwg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzqx8ok7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqx8ok7m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplqv080ju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqv080ju/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_o52s2jv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_o52s2jv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4o4z22ec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4o4z22ec/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvx8mcy43/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvx8mcy43/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpedmmsv_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedmmsv_f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe3uqomqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe3uqomqq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1te4qc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1te4qc6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp25s6ilj0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25s6ilj0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqf8dc58a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqf8dc58a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplaus_1cd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplaus_1cd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0__kj9p6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0__kj9p6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbj5629r8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbj5629r8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe1fw592x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1fw592x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp92gt7mr1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92gt7mr1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm6cfktdh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6cfktdh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp91of1b1_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91of1b1_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpben02adi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpben02adi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjtlbke77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjtlbke77/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprfiyuccp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprfiyuccp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf3sdjpn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf3sdjpn0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1050 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1050 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 1050 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 1050 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 1050 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 1050 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpywyiu66m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpywyiu66m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjhz0w1e_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhz0w1e_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9bqlagt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9bqlagt7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9o8vta00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9o8vta00/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt55w6r67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt55w6r67/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzszpjy9g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzszpjy9g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxmtvulwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmtvulwk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdzp2xu6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzp2xu6_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7913sabq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7913sabq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4z3ee7l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4z3ee7l_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdtkqgrrb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdtkqgrrb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn7y30b1y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7y30b1y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2kmoie5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kmoie5g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxlkjyld0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlkjyld0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4hl9_otk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4hl9_otk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsc7z1r3v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsc7z1r3v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9xa8d8uf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xa8d8uf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprxzqokgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxzqokgu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgnth79zf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnth79zf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfog3sas3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfog3sas3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkh3zwkt3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkh3zwkt3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr7x7xv5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7x7xv5c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoxdkd6x7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxdkd6x7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain121-method_chain121] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7443 | 9238 | a | 0 | + | E | chr5 | 7443 | 7702 | a | 0 | + | E | chr5 | 7443 | 9238 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3 | 4 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY+GJTtVkY2M84cIoNJ2FlYGTEQgYGFgYWBlkhQQYGBmZGBjYgZiRWZgBCBgZ2BgYmIAQChgZ+BhEGRkBwrADcA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain74-method_chain74] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1793 | 1805 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 77388 | 77734 | a | 0 | + | E | chr1 | 77388 | 77734 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2TgYmBkACJGBnYGhjwGbiBbv2UZJ6Nx/bQLIHFWRj1vBg7GSAYIkAERjACMUgUK') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________ test_nearest[downstream-True-opposite] ____________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 257 | 514 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1311528 | 1319231 | a | 0 | + | | | chr1 | 1311528 | 1319231 | a | 0 | + | | | chr1 | 1311528 | 1319231 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 125 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2SUYmJkAAEmBiDNBmIzGrivYmQs5lnCzljGwCgAFGAwFmFWZ2CQE2MEKQIAV+cDqA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 126 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAAnYGCGCEEwyMjAyYAAAB1gAN') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 461 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAAkYGBiQKxGCEs5EAAADfAAc=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_nj4kcw2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_nj4kcw2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuf_r1t4r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuf_r1t4r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa4a1csu0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4a1csu0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9bf6xq_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9bf6xq_6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvqcrsg0g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvqcrsg0g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjxm33rr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxm33rr4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdqmeohdt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqmeohdt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8baez9v8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8baez9v8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp49kmu_z6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp49kmu_z6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ddk2wxe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ddk2wxe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwi4ac8zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwi4ac8zc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwwfsjvxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwfsjvxv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpofz9nb6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofz9nb6v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo9iuyzi9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo9iuyzi9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv5kyi4y9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5kyi4y9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3zzdyz9a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zzdyz9a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpox7vu2mk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpox7vu2mk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5q8e0bme/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5q8e0bme/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz0oty2i3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0oty2i3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfghkqmre/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfghkqmre/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1tq94e1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tq94e1e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpok13ifh4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpok13ifh4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnmu_xzz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmu_xzz8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp362wvmz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp362wvmz1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp741he0ph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp741he0ph/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfd8l_vso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfd8l_vso/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxz9hbxs3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxz9hbxs3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6518ly_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6518ly_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyyiktbly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyyiktbly/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcgc6pdtt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgc6pdtt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpufqvtqcp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufqvtqcp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdpc_02gd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdpc_02gd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg11qvfrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg11qvfrg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2tjrr61d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2tjrr61d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvsgu8j_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsgu8j_3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuowc3z15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuowc3z15/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkvch_ozs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvch_ozs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy67dy2sy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy67dy2sy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1x81r9or/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1x81r9or/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_nja0mr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_nja0mr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjpe2zo9o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpe2zo9o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchlq2tgq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchlq2tgq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkt1f9grq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkt1f9grq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfvwdnsgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvwdnsgf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsen4kxa7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsen4kxa7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprq0m7crt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprq0m7crt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv4_rxswn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv4_rxswn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9lw04f2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9lw04f2m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp20k4sl6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20k4sl6d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdim6yqa9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdim6yqa9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpobwctyxa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobwctyxa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyccgrzf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyccgrzf8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx8cjct_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8cjct_a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplqzzjk1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqzzjk1i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3cvrnxxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cvrnxxo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvcdvuxva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcdvuxva/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplbtb37l0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbtb37l0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4i2dbjyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4i2dbjyu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnfjbgikl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfjbgikl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp82_p7ysm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82_p7ysm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi3wegtzu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3wegtzu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppwlwnhu1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwlwnhu1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwjf3cci3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjf3cci3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1hyo1dlt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1hyo1dlt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaj5rfzho/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaj5rfzho/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpanquqxs0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpanquqxs0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_41yffrx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_41yffrx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpns63y7jb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpns63y7jb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjkvukidk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjkvukidk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm3r0a9p8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3r0a9p8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1el6si_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1el6si_o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqcrevalp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqcrevalp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnxm7gqyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxm7gqyw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpirnmg2o5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpirnmg2o5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmputxk6od9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputxk6od9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe_fupm9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_fupm9w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppjocup9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjocup9s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc20pdhet/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc20pdhet/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt_0k2337/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_0k2337/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6huydeo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6huydeo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplbmx_5rt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbmx_5rt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5cj39e08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5cj39e08/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3fecx_xr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3fecx_xr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0w52jxsk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0w52jxsk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp81e4cclv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81e4cclv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7xc62cu4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xc62cu4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz5jk3k3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5jk3k3i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8j0a6ru9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8j0a6ru9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8n5i40dt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8n5i40dt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9tl60q9a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tl60q9a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjcvbeiyz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjcvbeiyz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplijjg6au/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplijjg6au/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3pfngvyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3pfngvyt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7c0beww4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7c0beww4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdqzj22rb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqzj22rb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpekknyqqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpekknyqqr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppkotyde1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppkotyde1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdlpahb8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlpahb8d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp_ljcvd5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_ljcvd5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ua_hvbt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ua_hvbt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptg6kmqvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptg6kmqvq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpswuxlg38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpswuxlg38/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzpbf81in/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzpbf81in/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxysy2i1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxysy2i1a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt40uov5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt40uov5h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpykz0h27x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpykz0h27x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpraddgkia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpraddgkia/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vbisfid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vbisfid/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp9y20578/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp9y20578/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkk3y1daa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkk3y1daa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6opp_7tm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6opp_7tm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy0l6jw5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0l6jw5d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwmxv5xga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmxv5xga/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpegkptwp7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegkptwp7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpef2_cmhf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpef2_cmhf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqrz03sea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrz03sea/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx32topwi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx32topwi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5iy8_1i9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5iy8_1i9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1s6i_xqi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1s6i_xqi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain122-method_chain122] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 327981 | 327985 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2031873 | 2033410 | a | 0 | + | E | chr2 | 724485 | 729639 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RgYwACRgYGVkYdIMUMZDNxc7Ex2rCIMYOEGcGyHNx8LAy88owgrogiIyMbWBdYEkwCADMYAVI=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain164-method_chain164] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 68618 | 78152 | a | 0 | + | E | chr1 | 68618 | 78152 | a | 0 | + | E | chr1 | 68618 | 78152 | a | 0 | - | E | chr2 | 68618 | 71959 | a | 0 | + | E | chr8 | 68618 | 78152 | a | 0 | + | E | chr16 | 68618 | 71961 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2688513 | 2691342 | a | 0 | + | E | chr1 | 131369 | 134454 | a | 0 | + | E | chr1 | 655936 | 658765 | a | 0 | + | E | chr1 | 2884884 | 2887713 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr1 | 68618 | 70168 | a | 0 | + | E | chr1 | 2333 | 2334 | a | 0 | + | E | chr1 | 291 | 3120 | a | 0 | + | E | chr1 | 852771 | 855600 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65582 | 65595 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 43 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicJY9BTgMxDEW/YzuZTJIJCFFaaRajiqJpxQgogkUBsWXdWyDWbDgAx+gZWHIYDkMCtiXbkr/9zI35OfD76/Ge9WjxafT88M37uxfLF18r8wFAGNko3GRBDkKgHaMaRd9bmqXYcJc6vK2eBsZaQUWDKCSqZYptSs6U4pYj58R01bKzOBNYQxvQqDSIeCJqSmva0IwOkzwSNMTOUvo/u7bQpuxeZp17LLoQo86ZLvVEJRN6oWBobE2J5we+phs/JF4WJXzvfcgutrrjLba2cqOjWYyS5TTh3oaKuKuIoSKWD+sLhaikv5gQi9MvFwMS5A==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 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('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 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('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain75-method_chain75] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 6657 | 6658 | a | 0 | - | | | chr1 | 6657 | 7189 | a | 0 | - | | | chr1 | 73483 | 80398 | a | 0 | - | | | chr6 | 65793 | 72708 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 161788 | 162048 | a | 0 | - | | | chr1 | 10000000 | 10000260 | a | 0 | - | | | chr1 | 707310 | 707570 | a | 0 | - | | | chr1 | 2 | 262 | a | 0 | - | | | chr1 | 2 | 262 | a | 0 | - | | | chr3 | 2 | 262 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicJYuxCQJREERnZm8/3wsEOQX5gtahBRgbeiDYgamJcLGxIBZhCVbg1WIFJu4hDMzweMPjtW+9ZN+kyajf2+n54u62hQteQFACiaRsxlUdWCiYo0Hgap3VYLYIRRzHgxaUyZA8TFNMH8QhITlanb9LO9TvTwBdHvcO0xD+z6EBVMAP8ekOwQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 | (and 86 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFArKnjGtDk0MAB1OAbI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 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('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_nearest[downstream-False-False] _____________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 nearest_how = 'downstream', overlap = False, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:115: in _nearest r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, pyranges/methods/nearest.py:62: in _next_nonoverlapping r_idx, dist = nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how='downstream', E overlap=False, E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:115 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:34: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp7se72q6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7se72q6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjb98m6b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjb98m6b3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd94fc_hj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd94fc_hj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcex6hd9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcex6hd9z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsy9rh3j4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsy9rh3j4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkbonq6rd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbonq6rd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7wyol_bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7wyol_bi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoozvv20i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoozvv20i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxhyxk6uu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhyxk6uu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp42oo2guw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42oo2guw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp13onfwoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp13onfwoy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgwps1liw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgwps1liw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1s3lks5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1s3lks5n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpylbh2goz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpylbh2goz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw6vbdexb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6vbdexb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8qw2eqqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8qw2eqqg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpud76306m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpud76306m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxgq47d0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgq47d0m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc2cwz28p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2cwz28p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptb4msfgx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptb4msfgx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp52tkqypa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp52tkqypa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp5sa6kzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp5sa6kzc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6fbopfvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6fbopfvl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiyg6ydpq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiyg6ydpq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_5l239m9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5l239m9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5y3b_qkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5y3b_qkd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8buyonq1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8buyonq1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiewhf56v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiewhf56v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_5qxbvaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5qxbvaa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9v22_n3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9v22_n3l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsydssmdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsydssmdq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuk2we0g1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuk2we0g1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3d296sx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3d296sx5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdc0unm4d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc0unm4d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx169wb_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx169wb_2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpad9xd5zu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpad9xd5zu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqyac7ncc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqyac7ncc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf7ny171j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf7ny171j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzr0akh2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzr0akh2i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmmiko0rq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmiko0rq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdrgl2g53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrgl2g53/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxytqjpk8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxytqjpk8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpygp87gfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygp87gfc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjh2syw_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh2syw_5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2wlxs5cv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wlxs5cv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0w2bcrk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0w2bcrk3/f2.bed) __________ test_three_in_a_row[strandedness_chain123-method_chain123] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9882556 | 9882820 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 258 | 515 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY7HhNeJjAAHjaad3MzAysjMC2YyMDCyGDOxgcUYgjxdEQTlsDCxMlgwAjnwDfQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain76-method_chain76] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 655620 | 655651 | a | 0 | + | E | chr1 | 655620 | 662304 | a | 0 | + | E | chr1 | 655620 | 655735 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65538 | 65540 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY8wXdO9kkV4d9ECFYy07Qx0DAyMIxXExMjMxM/pISTMyMTIUyTI4MsgxMDAwMTIBSWYGMGCEQjCTDSIGAKV1BqY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3887867 | 3888436 | a | 0 | ... | | chr1 | 3887867 | 3893634 | a | 0 | ... | | chr9 | 9340132 | 9346833 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 5 more.) ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5087215 | 5087629 | a | 0 | ... | | chr1 | 6291837 | 6292110 | a | 0 | ... | | chr1 | 9343932 | 9350405 | a | 0 | ... | | chr1 | 5651030 | 5657503 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 1 | 6474 | a | 0 | ... | | chr14 | 7539582 | 7546055 | a | 0 | ... | | chr19 | 8319362 | 8325835 | a | 0 | ... | | chrY | 2957605 | 2964168 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 17 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 5 more.) ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain194-method_chain194] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'subtract'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 592137 | 598288 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7 | 265 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY4zRn67PwMDIyJDEycnBwMggIsEG5AIhH4MqK4jBzMDABBYAATYGZqBSBgBn6QJS') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain166-method_chain166] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 149 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain124-method_chain124] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 402140 | 412139 | a | 0 | + | | | chr1 | 2 | 6049 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 980052 | 980568 | a | 0 | + | | | chr1 | 980052 | 986886 | a | 0 | + | | | chr1 | 8737451 | 8745784 | a | 0 | + | | | chr1 | 980052 | 980568 | a | 0 | - | | | chr1 | 980052 | 980568 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 32 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAEl5ayzrGGoJXA0AiypbLMxO+0ABwABDAEBAA0ATcQ9rAYi2wEABgF+AAABAAMAfycODAEzF54AAAAEcHx6/gMAvaq5PC2pAxKRN6AGHTvNgQF5NZqwAA4HAQERAwEcBQYAARoFBgAJBwYAHQIBEQcHBQQBAAEHBQUDH8DE2oVSqgEGBgcGAx0DGgcDGQUDAFwO9FMKA1wrFiCMEwInGrEHAhADGQIQAgsDAAMCAxkCABMDABYDAQAAAAEAAX+Yln4wAEcB') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 980052 | 980568 | a | 0 | ... | | chr1 | 980052 | 986886 | a | 0 | ... | | chr1 | 8737451 | 8745784 | a | 0 | ... | | chr1 | 980052 | 980568 | a | 0 | ... | | chr1 | 980052 | 980568 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain77-method_chain77] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:54 E (and 75 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain196-method_chain196] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 252 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain168-method_chain168] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 72709 | 78982 | a | 0 | - | | | chr11 | 133125 | 141327 | a | 0 | - | | | chr14 | 3841 | 10114 | a | 0 | - | | | chr19 | 1 | 6274 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 393219 | 394760 | a | 0 | + | | | chr1 | 8786808 | 8788349 | a | 0 | + | | | chr1 | 4765863 | 4767404 | a | 0 | + | | | chr1 | 4927854 | 4929395 | a | 0 | + | | | ... | ... | ... | ... | ... | ... | | | chr1 | 1050370 | 1052933 | a | 0 | + | | | chr1 | 458832 | 460116 | a | 0 | + | | | chr1 | 458832 | 460373 | a | 0 | + | | | chr1 | 458832 | 460373 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr7 | 1835278 | 1839122 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 182 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicJY+9SgNRGERnvu/+JDe5uzGLcSExWMkGsQhKQBBsRSGCINhaiIVJo4WCIFYWFtY+gVhrkyeIaG2TVvAZxM4Vm5nucA5ba/OnZrw+/dTj+9b3/9RXTwSBaEZhBQheESFi2DEJcqmYoIoUClwBMIiDt6UqQn6TCRckU3ppqyW6okzoQHgkRCpsizWoyaIDUke1FiUbdscWMzZfzn6evoZ302UZnW/M7PDo8tmOrt8TZCQ9wGAYlcKmBeollQX3b7MLo73Xh8lufzxnXOPwo+tMw3PTFVpF5iCsycH25BFtj71BiDF4sbpS89aZIFvV8gz/MkREUea60hYdRiDvIy31fgGoTiRI') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 247 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2CAA0YUCpcQAACVAAU=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain125-method_chain125] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 1 | 258 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1901057 | 1902132 | a | 0 | + | E | chr2 | 1901057 | 1902132 | a | 0 | + | E | chr2 | 136708 | 137783 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY4v6fHybJXceAzcDAyMDAwsDCAAZDMyswoyxjB7sLHZMiixs4gyMjEBRRkYmYyYxZgYxWSYgh8UIrJaJQYBDmYEBAENJBeI=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain78-method_chain78] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'set_intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1902337 | 1902880 | a | 0 | + | E | chr1 | 69379 | 73222 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 271 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicHYuxEUBQFAT3zoxHwI8FGEpQjl4ow8hUKfe/bHdvrl6e6riv0La/EWFLQIfGoKHVoGRE5cm5J/f/LjM3BYzXMzs9RfORD2VcBbs=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain197-method_chain197] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 135 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain169-method_chain169] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 89190 | 90983 | a | 0 | - | | | chr1 | 89190 | 89961 | a | 0 | - | | | chr18 | 89190 | 95197 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 655361 | 655369 | a | 0 | + | | | chr1 | 196610 | 196611 | a | 0 | + | | | chr1 | 655361 | 655362 | a | 0 | + | | | chr8 | 655361 | 655362 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAV1PQrsA1yo04/4/H0cXG8EfZiWfwAJAgAZERsCBgABEAMDAhgDAhACGwMAAAEAEwFcZRUDAgI9uRd2FQMBEwMCCQAGMFMHAAAAAQVCMJQwBT1qDekEAwAfCgIAAA4BABoCAAcCAQEaAwEJAhEBAAEDAVbabAADAAEAAAoAABAAAAAHAAAAAAAAAAEABgQBMQMBAQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr8 | 4097 | 9857 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 135 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAAAAAEaAQEJFgIAAAEAAQAAAAAABwAKABAAAAE1mBZ/AAA=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain126-method_chain126] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65545 | 65803 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 393331 | 393332 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 E (and 314 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2CM5lpz3El8LgOjt/HmaQwMjCDEwcDECGKkpfYygIXYGIoYRIFMBgDTBgaN') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain198-method_chain198] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain80-method_chain80] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2150838 | 2157144 | a | 0 | - | E | chr11 | 9763381 | 9766496 | a | 0 | - | E | chr15 | 2150838 | 2151137 | a | 0 | - | E | chr15 | 7177121 | 7187121 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr15 | 3997570 | 4000397 | a | 0 | - | E | chr15 | 2150838 | 2154817 | a | 0 | - | E | chr15 | 3650913 | 3653475 | a | 0 | - | E | chr15 | 2150838 | 2155774 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 589835 | 590861 | a | 0 | + | E | chr1 | 8229008 | 8232095 | a | 0 | + | E | chr1 | 289140 | 290165 | a | 0 | - | E | chr1 | 2156648 | 2159988 | a | 0 | - | E | chr2 | 7032356 | 7038506 | a | 0 | - | E | chr6 | 2286528 | 2292678 | a | 0 | - | E | chr6 | 67593 | 73743 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5714756 | 5721580 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'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') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7177121 | 7187121 | a | 0 | ... | | chr1 | 9869322 | 9869427 | a | 0 | ... | | chr1 | 2150838 | 2157144 | a | 0 | ... | | chr1 | 2150838 | 2155774 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr15 | 2150838 | 2154817 | a | 0 | ... | | chr15 | 2150838 | 2153604 | a | 0 | ... | | chr15 | 3997570 | 3997632 | a | 0 | ... | | chr15 | 3650913 | 3657749 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4740306 | 4742076 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain170-method_chain170] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2689793 | 2689794 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4063494 | 4063858 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2SOZmRhYGQAAVNNbgYIk9GKhZsJSDEycNoxsjIwsDFmAyUYgULSzIxsDAA6mQIG') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain127-method_chain127] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain199-method_chain199] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain171-method_chain171] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 921357 | 921359 | a | 0 | + | E | chr1 | 921357 | 921359 | a | 0 | - | E | chr1 | 921357 | 921359 | a | 0 | - | E | chr1 | 921357 | 921359 | a | 0 | - | E | chr7 | 921357 | 921359 | a | 0 | - | E | chr11 | 921357 | 921359 | a | 0 | - | E | chr11 | 921357 | 921359 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 211969 | 211970 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 171 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAUV8JiMwM2mR3HtA3czH8cDSemnBHCyzQFgBn+YBn4AAAEDd2WhwwQEQpN9AAMCARMAARcDATIGAAYBABABAQAACgAKDg8MAC8AASwBATQHAAABAQABBQADCgMADQABAAACAzwAAQAHAAAAAAAAAAIKCgAfASEAAA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain82-method_chain82] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8257537 | 8257538 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 69390 | 69435 | a | 0 | - | E | chr5 | 69390 | 69435 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgYGTM4GJgYGJkBDIZwICtjgEKGAslsw4y1syYVs9YCyRAClgYgTqANAcjPy8DL4MOSBuQDwAM2wd0') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10009667 | a | 0 | + | | chr11 | 7263309 | 7270278 | a | 0 | - | | chr12 | 5043703 | 5050761 | a | 0 | + | | chr20 | 7190041 | 7198218 | a | 0 | + | | chr20 | 2084875 | 2087312 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain200-method_chain200] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 194 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain131-method_chain131] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6793738 | 6793739 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 8 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2AAAUYowcgEorjTV3EyMIOFIhlYGGAqGIGQlYERACjzAZY=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain172-method_chain172] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 1794 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3232 | 3233 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY1RWTWFgYGAEQhDFDmYxeqTXi4IEWRl45jNAACOUZgAAT8cCsA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain201-method_chain201] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3.12/typing.py:1176 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 127 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain84-method_chain84] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 124 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain173-method_chain173] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 14 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 24 | 25 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 30 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RgBEI44GDgYWBkFJvoy8sAERZnQAcAISMBMw==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 258 | 271 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 6424 | 6426 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:378 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgYGUT71FkBAIGEAQBFgYgh4OBB0iJTfTlZQALS4qDxBkYADmlAik=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 14 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 14 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 14 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain133-method_chain133] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 131 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain202-method_chain202] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain85-method_chain85] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 114 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain203-method_chain203] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 113 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain134-method_chain134] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain174-method_chain174] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8472463 | 8472724 | a | 0 | - | E | chr1 | 131073 | 131334 | a | 0 | - | E | chr1 | 131073 | 131334 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3014659 | 3016455 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY4sN5JvB4rxxwyl+g6tMguIMQMAoycyQ1ejex8IMZDOBBIyZGFnkGBiZGRkZGFkk+BjYQMqYGJj0gAQLAzM7MwMjSISBnZGdid2ah5kBACbcCCo=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain86-method_chain86] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3.12/typing.py:1176 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 98 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain204-method_chain204] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain135-method_chain135] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain175-method_chain175] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 513 | 525 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 216 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAABAgMAABcAAAEAAQI/BQoAAAAAABsAAgAAAwALAAE=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain87-method_chain87] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain205-method_chain205] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain176-method_chain176] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain136-method_chain136] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain88-method_chain88] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 4 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgEAGRmYmRhAFZjPkgygGAAPWAIA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain206-method_chain206] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain137-method_chain137] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain89-method_chain89] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 259 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 264 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 65537 | 65544 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 514 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 259 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 259 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 10 | a | 0 | - | | chr1 | 3 | 10 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 259 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 257 | 770 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 2 | 4 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 1 | 258 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 258 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 10 | a | 0 | - | | chr1 | 3 | 10 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 259 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65539 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65540 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 514 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65539 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65794 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 258 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 258 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain180-method_chain180] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain207-method_chain207] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain138-method_chain138] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131331 | 131367 | a | 0 | + | E | chr1 | 131331 | 131367 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2AUYXLKZuSWYWBkAALGOiCGQgYmRiYGFgZloDAAKsUBnQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65538 | 65797 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 771 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 257 | 516 | a | 0 | + | | chr2 | 257 | 516 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 8966 | 9224 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 8966 | 9224 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131367 | a | 0 | + | | chr1 | 131331 | 131367 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131367 | a | 0 | + | | chr1 | 131331 | 131367 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131367 | a | 0 | + | | chr1 | 131331 | 131367 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131333 | a | 0 | + | | chr1 | 131331 | 131333 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131367 | a | 0 | + | | chr1 | 131331 | 131367 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131367 | a | 0 | + | | chr1 | 131331 | 131367 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131367 | a | 0 | + | | chr1 | 131331 | 131367 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131367 | a | 0 | + | | chr1 | 131331 | 131367 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131331 | 131367 | a | 0 | + | | chr1 | 131331 | 131367 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain90-method_chain90] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain208-method_chain208] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain182-method_chain182] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 127 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain139-method_chain139] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131076 | 131589 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAABBgIAAQABCwEBAAABAAAAAQAPAgADAB8CAAAAAA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain91-method_chain91] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:43 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain209-method_chain209] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain183-method_chain183] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain140-method_chain140] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 4 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:65 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgcGW1q2IAAXYGOOCFcpmAGAAf8QEg') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain92-method_chain92] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 270597 | 271945 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 401183 | 401184 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkZGBgEGEQZgDRIAwkmFgUWYCUGqszkARCUUY+BjCLgZFNXo6BA6QKAB/RATw=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain210-method_chain210] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1310731 | 1311502 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:43 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAABGI0AAAEBAQAABAAIAAEAAAEAABQACgAAAwIAAA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain184-method_chain184] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1965369 | 1971227 | a | 0 | - | E | chr18 | 1965369 | 1971227 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr19 | 852325 | 854118 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:293 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgZGBg4AURjEZ8GksZU5PfBYHEBBkZgWSu7F8LBkGxh4xAIUZGD5cPk0FyQkDFvIwpjAyp7AwgCQYAR6oJCw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain211-method_chain211] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain185-method_chain185] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain141-method_chain141] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 77 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain96-method_chain96] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 80 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain186-method_chain186] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain98-method_chain98] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 248 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain143-method_chain143] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2019888 | 2019938 | a | 0 | - | E | chr20 | 2019888 | 2019938 | a | 0 | + | E | chr20 | 2393321 | 2393371 | a | 0 | + | E | chr20 | 2019888 | 2019938 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr20 | 2019888 | 2019938 | a | 0 | - | E | chr20 | 2019888 | 2019938 | a | 0 | - | E | chr20 | 2019888 | 2019938 | a | 0 | - | E | chr20 | 3963233 | 3963283 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3963233 | 3971124 | a | 0 | + | E | chr1 | 1115040 | 1122931 | a | 0 | - | E | chr1 | 1115040 | 1122931 | a | 0 | - | E | chr2 | 1115040 | 1116481 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr20 | 1115040 | 1122931 | a | 0 | + | E | chr20 | 1115040 | 1122931 | a | 0 | - | E | chr20 | 1115040 | 1122668 | a | 0 | - | E | chr20 | 1115040 | 1122931 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4309751 | 4317642 | a | 0 | + | E | chr20 | 2393321 | 2394249 | a | 0 | + | E | chr20 | 4309751 | 4317642 | a | 0 | + | E | chr20 | 4309751 | 4317642 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr20 | 4309751 | 4317642 | a | 0 | + | E | chr20 | 3963233 | 3971124 | a | 0 | + | E | chr20 | 4309751 | 4317642 | a | 0 | - | E | chr20 | 4309751 | 4313595 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY+WMfcrFJHfO51TrgR1shqea9JbNunCwIscj8BZjom3bVXbWmHVOCg8lQ0p7DzLVz5hWx6KYcn0mo5Pxk6dsySdXn3O5v5RZP2blPgZebi5eNkYGBmkpeWEeTmWbygRpRlGVlhdcnAwKcpf0GUwYDIGyIBWMjFArmVghVrKpzbrACLSSkQloJRsr0Eo2JqCVLCAr2RnEgFayhM9kYGJmYGVj5uTmY2BkZWDk4WSAWinIxCjLhtVeRkHm+fy8rDFavqwLbJiTZE/b8DHzM4OcI8DMCDSGn4NBkhPiMBM2Rgl2RiUGNm4WBkNuPiZGTlZGBiaiHEZaWGg5Hvqmz8+F5jS4q4A+Y2AAAAMGWZ4=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr20 | 2393321 | 2394249 | a | 0 | ... | | chr20 | 3963233 | 3972016 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr20 | 2393321 | 2393371 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain215-method_chain215] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain99-method_chain99] ___________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain187-method_chain187] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E (and 121 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain145-method_chain145] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr3 | 18 | 4910 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr7 | 2162689 | 2163203 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAAAFmcDYzU7GAAAAQEXAwEAAAACAAAAABEAABMbAAABWk5SkAAAAAYAMiEAAAAAAgEAAQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain217-method_chain217] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2360577 | 2360835 | a | 0 | + | | | chr14 | 4135937 | 4136194 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1991393 | 1992974 | a | 0 | - | | | chr7 | 8127005 | 8128586 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr8 | 143105 | 143110 | a | 0 | + | | | chr8 | 2688807 | 2689346 | a | 0 | - | | | chr14 | 4142025 | 4144074 | a | 0 | + | | | chr15 | 1191220 | 1192541 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 167 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicHY4xakJBGIRn/t39dyM+fVhISB4vKCJRFAutxGCTW4iF5hBpFMklRE2R3hOEVAEbT2AdSG+TA8TFZgbmG4axT9+j7WByMC/v++ffv/PHV3mX5rXVwnvjycCyAgkUdpwhAMWGi2YIBEZhJsh0eIWEFkGQtwvJEgak+fwH6LbetBO7GhPCLjfrlXXTTyez/xNKQmsoHjRILFHSOJr7lK+Vbl+NjvvHGxHp4R7S8k1U2XaPnsIcdbmjKQQ8OHTiPQWdAXAB+iwasw==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 3330 | 11109 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 258 | 1346 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 | (and 175 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkYNJkZ2CQYWBksZdhYGAEQwYGXiAhIJcEFLBlZ2SEijMysLHYMzAAADIKAeU=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain100-method_chain100] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 180 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain188-method_chain188] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain147-method_chain147] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 257 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain218-method_chain218] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 76802 | 86026 | a | 0 | + | | | chr1 | 630046 | 635985 | a | 0 | + | | | chr17 | 630046 | 638592 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1474429 | 1483182 | a | 0 | + | | | chr1 | 1474429 | 1480838 | a | 0 | - | | | chr3 | 1474429 | 1482968 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 290228 | 290351 | a | 0 | - | | | chr6 | 1178 | 1181 | a | 0 | + | | | chrM | 329068 | 329071 | a | 0 | + | | | chrM | 203614 | 203617 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicPY+rTgNRGIRn/jmXbdOmG7ILvS8lyIVADZsgVuEwGARJBZKQWgQhKQKNJEGg+wC8CLwRpwYxI0bMzOdOft9Or55erV7b1rer9xsY2REDx5wA+QhVlxRHrFlwj5Vdd75mNF1cHizN5ozHEQ+Le8ANPzZ9K9vtoY0lYqCdz60ngTOhygAM9zcvQ2tHWUm/uMvFuWTRuhYM53VY4uhMQJUGOQVI9h3YeBYhsIlOPvO71Au+I6cgJqXangLcZ8nbn6bv1t9RpbxyFN4/FlZrskJO4Tk9SHgc/ONxmpoYEx74BxvwF/M=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 | (and 61 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain101-method_chain101] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain189-method_chain189] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 248 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain148-method_chain148] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 201 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain102-method_chain102] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain219-method_chain219] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131071 | 131328 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65537 | 66305 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RgZ2ZiYARCBknG//8YGBkZuMBcoAAEgBhMTP8hLEYQZgAAZT0DPg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain190-method_chain190] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131074 | 132867 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgYGViYGRkYGRgABMQwATisAMZAAGTABg=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain149-method_chain149] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain103-method_chain103] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3.12/typing.py:1176 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain220-method_chain220] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131335 | 131592 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 26644 | 26901 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2Rl4nnGwMDIwMLEyAaiGRjYGXVAFAg4MGQIgwUZGRgZQZQYAyMAQ6gCFw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain104-method_chain104] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain150-method_chain150] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain192-method_chain192] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3361888 | 3364080 | a | 0 | + | E | chr1 | 346247 | 355426 | a | 0 | + | E | chr1 | 4520172 | 4522370 | a | 0 | + | E | chr1 | 6708964 | 6708965 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr1 | 3361888 | 3364086 | a | 0 | - | E | chr1 | 3361888 | 3370230 | a | 0 | - | E | chr1 | 3361888 | 3362330 | a | 0 | - | E | chr1 | 5573892 | 5578872 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3361888 | 3368804 | a | 0 | + | E | chr1 | 3361888 | 3365738 | a | 0 | + | E | chr7 | 3361888 | 3364080 | a | 0 | + | E | chr7 | 3361888 | 3368812 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr7 | 3361888 | 3361889 | a | 0 | + | E | chr7 | 3361888 | 3362406 | a | 0 | + | E | chr7 | 3361888 | 3362330 | a | 0 | + | E | chr7 | 3361888 | 3365488 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2817 | 4355 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E (and 41 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY3J/77ChpaSNRetWhYfoeUsmU6a3viyp92a9m7yEm41jf8y2pP2cTLFXRTqYW/LZqhgYGBgdN3hIPmkKigrtZA78uXDWpbY7Qk5Z7CwxW9x1l0ZZnZBsu5v1OPeSLoMMFwejIhMDCwMjK6f79lrFUF5mGTaVhYUz0+IeC/JzmrNwnZqj4PLjtQlT2G7TL41KnapcPMzxi7yOsnq02fJzqjObcTIEGfvE23Lzc3HoMe404BDnY9dncrVlq2Zg0OLm5/TU69f9buAsXKzPJsRmL8VoydFvr8ucpXxLg5VXYaohszQzB6MlH4cxhwEfhwkfKxM/pwo3L1O4Bqv0bxteTkVWTjY5dgZNXRH7JK1nHFPlORgVWBjkOWRYGTm42BmYuLnZ2Ti4OBm5+dlZGRkEePj5+Xg5+BkYJZgYhDnlebm4efn5OUw57Pj4GO15GZhoGI4gxUAnMLChBQc7KDhYedmsIcHBycfPy27ALGzMDwwOfi5ocGgxS3Gw8jKI4goOdmBwcPOgBwcD0DpGRiYgBYw+IGRl4Aa6goENyAYArEJ6UA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain221-method_chain221] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4gaCgNFQMzgMAARcACQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain105-method_chain105] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 127 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain151-method_chain151] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 194 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain222-method_chain222] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2162699 | 2162706 | a | 0 | + | | | chr1 | 2162699 | 2162706 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2162691 | 2162695 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 30 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY1Nk4GVgZOBgYGIAAS5FBi4gl40RSDCwgiV4YRJMQC4zHwMUMDICVTACACKSANw=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1966593 | 1969187 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1966593 | 1969187 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1966593 | 1969187 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1966593 | 1969187 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1966593 | 1969187 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 13 | 8462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 13 | 8462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 13 | 8462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 13 | 8462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 13 | 8462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain229-method_chain229] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgYGIQkuVX52dgYGTABAALvgB4') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain106-method_chain106] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain152-method_chain152] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 198 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain223-method_chain223] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8 | 1804 | a | 0 | - | E | chr1 | 8 | 1810 | a | 0 | - | E | chr1 | 8 | 1804 | a | 0 | - | E | chr1 | 8 | 1804 | a | 0 | - | E | chr1 | 8 | 1804 | a | 0 | - | E | chr1 | 8 | 3088 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 262145 | 262403 | a | 0 | + | E | chr1 | 262145 | 262403 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicJYqxDYAwEAN9ecIrIiIFBQUSW1CyCC01G1EwITMQwIXlkw9JRmB0YmcDbQmZbT9vjuUyYeiPw+yJuGavUB9kSfRQpLqb6sBro+lrHjWVBPM=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain107-method_chain107] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain153-method_chain153] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain231-method_chain231] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 126 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain108-method_chain108] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain154-method_chain154] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 123 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain232-method_chain232] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain224-method_chain224] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:54 E (and 66 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain109-method_chain109] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain155-method_chain155] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain233-method_chain233] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain225-method_chain225] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain110-method_chain110] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain156-method_chain156] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain234-method_chain234] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain280-method_chain280] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 137 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain111-method_chain111] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain255-method_chain255] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain281-method_chain281] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain235-method_chain235] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain112-method_chain112] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 328194 | 328451 | a | 0 | + | E | chr1 | 328194 | 328451 | a | 0 | + | E | chr3 | 328194 | 328451 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:18 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:20 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:23 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:28 E (and 236 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2AQs2W11TRiYGFgZLR/MZfRPG06O6MLgzQTAyNQBAiYGJgYGBhZmRiBJAMQKzJVgSgwhwGsCgD3TQUR') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain256-method_chain256] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain282-method_chain282] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E /usr/lib/python3/dist-packages/natsort/utils.py:500 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain236-method_chain236] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 131586 | 141061 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 131586 | 141061 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 131586 | 141061 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 131586 | 141061 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 131586 | 141061 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131586 | 141061 | a | 0 | + | | chr1 | 259 | 776 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131586 | 141061 | a | 0 | + | | chr1 | 259 | 776 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131586 | 141061 | a | 0 | + | | chr1 | 259 | 776 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | + | | chr1 | 131586 | 141061 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | + | | chr1 | 131586 | 141061 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 132099 | 132869 | a | 0 | + | | chr2 | 75011 | 75781 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 131586 | 141061 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 131586 | 141061 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 259 | 9734 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 259 | 9734 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 259 | 776 | a | 0 | - | | chr1 | 259 | 9734 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain113-method_chain113] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:293 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain257-method_chain257] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain283-method_chain283] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain237-method_chain237] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr3 | 513 | 518 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAAAABADAAAAAAABAQAUAwMAAAACAAYAAgAABwAEAAAA') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain258-method_chain258] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain302-method_chain302] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 173 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain284-method_chain284] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain303-method_chain303] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain259-method_chain259] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 E (and 311 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain238-method_chain238] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:43 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain304-method_chain304] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 135 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain285-method_chain285] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3585 | 5134 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 65537 | 65538 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 257 | 3330 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3585 | 5134 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 3330 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 3330 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 3330 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 1 | 3 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 1 | 3 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 1 | 3074 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 3330 | a | 0 | + | | chr1 | 257 | 3330 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3585 | 5134 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 917506 | 920579 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 3330 | a | 0 | + | | chr1 | 257 | 3330 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 3330 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 7 | 8 | a | 0 | - | | chr15 | 7 | 8 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 7 | 8 | a | 0 | - | | chr15 | 7 | 8 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 7 | 8 | a | 0 | - | | chr15 | 7 | 8 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 7 | 8 | a | 0 | - | | chr15 | 7 | 8 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain305-method_chain305] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain260-method_chain260] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain239-method_chain239] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain306-method_chain306] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 174 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain286-method_chain286] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain262-method_chain262] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 771 | a | 0 | + | E | chr1 | 1 | 771 | a | 0 | + | E | chr1 | 1 | 771 | a | 0 | + | E | chr1 | 1 | 771 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5997563 | 5997564 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAAkYQZgRSjCAWE5gBZDEygfkIAFEDUU+kJmawIANjkicDP0iPUnTzL4gMACktAuU=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain307-method_chain307] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 136 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain241-method_chain241] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 73268 | 79157 | a | 0 | + | E | chr1 | 7161500 | 7167389 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7161500 | 7161513 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2319112 | 2320137 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYxRn4GZkzFKdKsAABIwMeblusxk4GOWMGVjFgVxGkBg3I0gKKgcS4wHxjUtlToCFbZWT2UHCLCBRAFIcB8g=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain287-method_chain287] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 911106 | 911140 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1246212 | 1253126 | a | 0 | + | E | chr1 | 1246212 | 1246727 | a | 0 | - | E | chr1 | 1246212 | 1253126 | a | 0 | - | E | chr1 | 1246212 | 1253126 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 E (and 367 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2DkZ2KUZhBkYmBkAANGhgre54wM3AyKIDYfEyMjgwBQ0iq2nYEx32KVJ0iUVZiFmZFBhIkJqEdRmhHIZmAEAL7SBTg=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain308-method_chain308] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 208 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain264-method_chain264] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain243-method_chain243] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | + | E | chr1 | 1 | 641 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 258 | 515 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2Bk4BFiAAFGJjYGRsYEXreFDIxABiMjUAgkzCjBVM/ABmIzRnGB1DKC5RlYQbIAYDcCtA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain288-method_chain288] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain309-method_chain309] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 145 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain245-method_chain245] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 250 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain266-method_chain266] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 513 | 862 | a | 0 | + | | | chr1 | 3278109 | 3278110 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 7337182 | 7337719 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2515689 | 2519020 | a | 0 | + | | | chr1 | 3410949 | 3414283 | a | 0 | + | | | chr1 | 207364 | 209417 | a | 0 | - | | | chr1 | 8008312 | 8012415 | a | 0 | - | | | chr1 | 4325890 | 4333386 | a | 0 | - | | | chr2 | 1353408 | 1360581 | a | 0 | + | | | chr6 | 8008312 | 8015808 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 171 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicHY+/L0NhGIXP+37v+93bq+1tU5EO1WrLpa4fSdMIuRgsBqEGxGAyMBiMEiFiJxIDNhObySDp4p+QSInBIOlKOhjdyFlOzpM8ybFHN1cnNF5/OEUa5AsRUkBdC+gBx5WBNK1OMm3BizkgGwz6jwXtdz/ggjgPjQczdHa87PBA30qNk92fp7fbpcv1tm627h6nXs6p2HzfpenMb8Kmyzs1DMeeqoWSUtUhwOfYUaDAUCiEhgw2kjKm1QWmCKWv+USw3Skxeu+fs46jTDkzavLsUoUqjM3PzvV3q31YP/AkSGlOMrwW7k1cRK8FaWA2xYFExmSsCzG+zLGKMUSJ0HPFOhISmv2LRUNJokjJtyjH123V+DrCWTvDnrIqoAL8AU2gLfk=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 721157 | 721159 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 15 | a | 0 | + | | | chr2 | 101902 | 101916 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 | (and 346 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2DgC/b4+FuW24qRkZGBiZEBBBkYuBlZgCSQxagdeegZo52UCiuYxwBUZMbYx8vIWM0AAjwMvAwMACfCByw=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain290-method_chain290] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 214020 | 214282 | a | 0 | + | E | chr1 | 214020 | 215597 | a | 0 | - | E | chr1 | 307 | 1884 | a | 0 | - | E | chr1 | 2623233 | 2623281 | a | 0 | - | E | chr1 | 214020 | 215597 | a | 0 | - | E | chr1 | 459016 | 466209 | a | 0 | - | E | chr1 | 3021320 | 3022897 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4486594 | 4488649 | a | 0 | + | E | chr1 | 1 | 7426 | a | 0 | + | E | chr1 | 1 | 4972 | a | 0 | - | E | chr1 | 1 | 8119 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2228738 | 2229509 | a | 0 | + | E | chr1 | 2228738 | 2229509 | a | 0 | - | E | chr1 | 2228738 | 2229509 | a | 0 | - | E | chr1 | 2228738 | 2229509 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicJY+9SgNxEMRnd293JZBElHjmjImIRRA0mBCRmPKqYKFVCsHSIhYWfhQSkFRprHyAFIKPINqKaGuX2kLwIRT0fzjlDMz8RjrbhRPn6tP5zXSlF182LbXftp3d/nxErfHRI+PgNdbDu5dpp9tyly7IhRTKBKpow8lVhQXUZJd+3bFue5uJIyepzAqjEVGpvU8a6aCyiLzVF5QSAkjXtOzUk/67Viefb9+nw+P8tSwV70chTLDxNdlJL55r0RUAldLWcHdceygDM2aEZRSY5gcwJhPKATGTGIpZMf8/QiTCxGFIKLMxt5oxCyshXAgK0H+9jCWB') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 307 | 1884 | a | 0 | ... | | chr1 | 307 | 1884 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain311-method_chain311] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9562568 | 9565131 | a | 0 | + | E | chr1 | 459009 | 461572 | a | 0 | + | E | chr1 | 9562568 | 9565131 | a | 0 | + | E | chr1 | 9562568 | 9565131 | a | 0 | + | E | chr1 | 9562568 | 9564873 | a | 0 | + | E | chr1 | 9562568 | 9565131 | a | 0 | + | E | chr1 | 9562568 | 9565131 | a | 0 | + | E | chr2 | 9562568 | 9565131 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9562568 | 9563337 | a | 0 | - | E | chr1 | 9562568 | 9563337 | a | 0 | - | E | chr1 | 9562568 | 9563337 | a | 0 | - | E | chr1 | 9562568 | 9563337 | a | 0 | - | E | chr1 | 9562568 | 9563337 | a | 0 | - | E | chr1 | 9562568 | 9563337 | a | 0 | - | E | chr1 | 9562568 | 9563337 | a | 0 | - | E | chr5 | 9562568 | 9563337 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1248769 | 1248771 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2TgYORhkWXmYWFlZWZmZ2JgYItmk/BjlWYKusPsuuSHTN2RxyyiXfMOscgpszIwsDACASsDIzMjMxsDAyODKJDNwMjCKMbOyMBQNvHlcUEWRk4GBmYuoEFgc1kImlu2023TbI1AkPECjIzcbIzMDFCTGayZGVmYGFg4kcwHmg2UZWRiYmMEqWIQ5mNg4AUxAKHyG/0=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain246-method_chain246] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 132 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain267-method_chain267] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 590082 | 590340 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 131844 | 131845 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RgYGZjAANORkYGBiBmZCyS0hEFMhkYmJiZGZgYkAEjIwAbiAD0') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 590082 | 590340 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 131844 | 131845 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 | (and 61 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2CAAkZGRgYGZjYIhxPEAWJGxiIpHVEgk4GBiZmZgQkkBwARewD0') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain292-method_chain292] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 79 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain247-method_chain247] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain313-method_chain313] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 135681 | 135693 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 328708 | 329734 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkYmBkAAFGRgEGHiDFwM0kxMDAxMANZAf7uBcDRYAKpFlZmBkYWIAsACS9Adg=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1545 | 9276 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain268-method_chain268] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2224641 | 2224642 | a | 0 | - | E | chr1 | 2224641 | 2224642 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66824 | 66827 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYxQy2yjKmJL4RY+BgZEhVvETAwMTA5DJyMDLwAMUYQRxWNmBNFiYlRUkwsgIANAUBKY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain248-method_chain248] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain294-method_chain294] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 280 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain269-method_chain269] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAAkYIZoSxwRxGRgibAUahAwAB9AAM') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain315-method_chain315] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65550 | 65842 | a | 0 | + | | | chr1 | 73586 | 83571 | a | 0 | - | | | chr10 | 197139 | 203288 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2592555 | 2600238 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 1228292 | 1228294 | a | 0 | - | | | chr15 | 1228292 | 1228294 | a | 0 | - | | | chr15 | 2024666 | 2025948 | a | 0 | - | | | chr15 | 197178 | 197180 | a | 0 | - | | | chr18 | 2403505 | 2403872 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 69 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicLY4xSgNhFIRn5v3/bpJl12TBEDRZ0QiBxASbFCm0t7RYvICIlWCfE2hh7wVsUlgJscg97CzsLHIFX8BqYJiZb3Ty/fy5+X0dD67TkF3U63C8vZzdf9zyX9Enmg0DCwpRhGim0gAiFw5NbR49ojIzXHHYhHnqZoQW67PV+bIXQHGPMHaNQJz0uQ95GenoZZxgUgme2VnKYr3mfPnUC8O5D7CQdzNHBacpFTpAYbo7Xb13DdXPVx6Vh8EbEtOiE5Pdh7Lc+D/jQ8sOpohEAdLJ/AM9rRzo') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 249 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain249-method_chain249] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain295-method_chain295] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain250-method_chain250] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3.12/typing.py:1176 E (and 132 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain296-method_chain296] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 236 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain270-method_chain270] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGOGBEYqNIQAEAAOAABg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain316-method_chain316] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 4075307 | 4077489 | a | 0 | - | | | chr16 | 9798742 | 9808294 | a | 0 | + | | | chr17 | 9999999 | 10000327 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 3163393 | 3170562 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 65 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AANqX8FQBU4ld3AEP/NLQEi8SQAZAgAQAQEBFgIHAwEfCQAPGwJ/mJZ+BAA0lYRVBgMBNz4vKgANABklTxsBAQiFBwEABwFHGQAAAAECHgMCFQAAAQMAKfYpBDBFAAAHAAEcAAABAAEAAAECAQAHBwIBAQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 134 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain251-method_chain251] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain297-method_chain297] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 243 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain317-method_chain317] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4AadQAVwQAADYAAY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain271-method_chain271] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 393473 | 398340 | a | 0 | + | | | chr1 | 393473 | 398340 | a | 0 | + | | | chr1 | 393473 | 400230 | a | 0 | - | | | chr4 | 393473 | 398340 | a | 0 | - | | | chr8 | 393473 | 398340 | a | 0 | + | | | chr12 | 393473 | 398340 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2509186 | 2517178 | a | 0 | + | | | chr1 | 4813333 | 4823332 | a | 0 | - | | | chr1 | 2509186 | 2509956 | a | 0 | - | | | chr2 | 9176379 | 9177149 | a | 0 | - | | | chr3 | 2509186 | 2512775 | a | 0 | - | | | chr4 | 2509186 | 2515361 | a | 0 | - | | | chr5 | 2509186 | 2511562 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5884552 | 5886545 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 190 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicTY+7LwNgFMXP+V43VaoofUnRNm2Epk0bRAkSgzTdsNhIKzEZOlVIGpPFLFZ/BVYiaNjYrQYjs68m4z2v3J+OttaS9uTyomN28/WkGt7Pr7u9u6Hrj8bjz+3r99FLvREwpc+t5+23KyQ080KK6JiCDFrocVKJKGsQjHICBMqOmNGzieaShhlRaaKgEAUCTLAP85zUHKMwK84gJEZUQRysqgJ0OAYMV5xhIJeidSoMq5vLXVfPHICWEWLAx/ywAgkWRVjy9aTygl5UU6KndcZ7gvDNXPH9/qHWihi2z211NetytdOybgc2+t1m5StkKvZwYmFUW3TyobgoFUul3T9C+JkeofGE/CP0X3vCeM9AEHanewZBVZ78SfwCavgrWA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 | (and 61 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain252-method_chain252] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 125 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain298-method_chain298] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 234 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain253-method_chain253] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain299-method_chain299] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain272-method_chain272] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4AaeQASNCEAAA4wAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain318-method_chain318] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAAUYghNBIFEwQBuA8AAFAAAk=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1162793 | 1171217 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 18 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain254-method_chain254] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain300-method_chain300] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 245 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain273-method_chain273] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:18 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:20 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:23 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:28 E (and 237 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain319-method_chain319] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4gU6hcQAA6QAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain321-method_chain321] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 278017 | 278019 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 67080 | 67081 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYzRmgAEWOxDJCERB3kyFEBYbO4MQRFCAgYPBgBnIBgA1bwH2') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain301-method_chain301] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain320-method_chain320] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') __________ test_three_in_a_row[strandedness_chain274-method_chain274] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain322-method_chain322] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 219 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain353-method_chain353] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain341-method_chain341] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain276-method_chain276] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3539970 | 3541291 | a | 0 | + | E | chr1 | 394760 | 396081 | a | 0 | + | E | chr1 | 394760 | 396081 | a | 0 | + | E | chr1 | 394760 | 396081 | a | 0 | + | E | chr1 | 394760 | 396081 | a | 0 | + | E | chr1 | 327697 | 329018 | a | 0 | + | E | chr1 | 1443587 | 1444908 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1443587 | 1444359 | a | 0 | + | E | chr1 | 337925 | 338697 | a | 0 | + | E | chr1 | 337925 | 338697 | a | 0 | + | E | chr1 | 394498 | 395270 | a | 0 | + | E | chr1 | 337925 | 338697 | a | 0 | + | E | chr1 | 1058306 | 1059078 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3074 | 3076 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 41 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYxZLWM3CKsGsrskSw5L1gC1c4xw7S+2MafUsbHUMDIwMzIwMDPJAmpGZgVOMnYmTjZ2VQUCNkdGMhZGBhY2NnYGHVYMFKMvMwMDAxMDCCARBi9mRjEng85qB1ShhBphhPMwCbKxASZBJzCCT2EAmgbQwMvAwgikGAPuAEDA=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 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('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges 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('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain354-method_chain354] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain323-method_chain323] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 91 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain343-method_chain343] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 246 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain355-method_chain355] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain278-method_chain278] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFArMBAAAWwAF') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain344-method_chain344] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain325-method_chain325] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 206854 | 207159 | a | 0 | + | E | chr1 | 206854 | 207159 | a | 0 | + | E | chr1 | 3606278 | 3606583 | a | 0 | + | E | chr1 | 458803 | 460088 | a | 0 | + | E | chr1 | 1 | 306 | a | 0 | + | E | chr1 | 206854 | 207159 | a | 0 | + | E | chr1 | 206854 | 215303 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 197391 | 197696 | a | 0 | + | E | chr1 | 458803 | 459108 | a | 0 | - | E | chr3 | 1771012 | 1771317 | a | 0 | + | E | chr4 | 8072193 | 8072498 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr5 | 1 | 306 | a | 0 | + | E | chr5 | 7968541 | 7968846 | a | 0 | + | E | chr5 | 4379667 | 4379972 | a | 0 | + | E | chr5 | 8330499 | 8330804 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2491649 | 2491906 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYzKr8wln1lq45ukfvtRlSiWPLp1b+MJWZGkKOyNX24NMVsFXJx02umY37o5jDMzf+Y5JWO/kJrZgGU05BgUWRgYGBhUWJyCpw8zKzmDExszKxGjOzspgyqzBysLMyMrCws5mp8ggw8zMxmDLaMDAwMSowczAyshox8QM1MzEVsfAwMikCLGbiSi7GYR5OBkYFNgYmHSYGYFmMAswm7EwcDEwsNhyiNXLMjEyBG9tvlKtw6DGy8YjzcbMxMPHIcTHxsju6nRFiJmHqQroWi52Rh6Ig7lZDSqny4AcyAdyIBMDgy4vyGXMrAzsQCMZQIoZGNVYQQyQbwGNcTqW') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges 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'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain356-method_chain356] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain345-method_chain345] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 174 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain366-method_chain366] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2SAAEY4AaMY4XxkJSAAAAEVAAg=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain327-method_chain327] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain357-method_chain357] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 217 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain346-method_chain346] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain367-method_chain367] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8323585 | 8326425 | a | 0 | + | E | chr1 | 7526102 | 7528942 | a | 0 | + | E | chr1 | 7526102 | 7528942 | a | 0 | + | E | chr1 | 8851928 | 8854768 | a | 0 | + | E | chr1 | 7526102 | 7528942 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 262402 | 262404 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 190 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY+TobPzGKJ0eJM/oZM6qz+hs3lbCmOTox8rAyMgIxAxi9UwMjMx57YLXGSKLrl1lMOcWZ2QAijAAiVg2/yNAioGBBaQWxABhEJ+BEQD1SAzw') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain329-method_chain329] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 199 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain358-method_chain358] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain347-method_chain347] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 174 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain368-method_chain368] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4gU6hcQAA6QAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain330-method_chain330] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 185 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain348-method_chain348] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain360-method_chain360] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7744690 | 7744691 | a | 0 | + | E | chr1 | 5502006 | 5502200 | a | 0 | + | E | chr1 | 4202035 | 4202036 | a | 0 | + | E | chr1 | 3644225 | 3650605 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr1 | 3451000 | 3453950 | a | 0 | + | E | chr1 | 2976561 | 2983042 | a | 0 | + | E | chr1 | 1638395 | 1641986 | a | 0 | + | E | chr1 | 38532 | 40154 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7744690 | 7751355 | a | 0 | + | E | chr1 | 4202035 | 4208700 | a | 0 | + | E | chr1 | 5565989 | 5572654 | a | 0 | + | E | chr1 | 3644225 | 3650890 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr1 | 3644225 | 3650890 | a | 0 | + | E | chr1 | 3451000 | 3453950 | a | 0 | + | E | chr1 | 2976561 | 2983226 | a | 0 | + | E | chr1 | 38532 | 39314 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 4868 | a | 0 | - | E | chr7 | 1 | 4868 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 44 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'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') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 402883 | 402884 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr4 | 402883 | 403874 | a | 0 | ... | | chr6 | 402883 | 403874 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 402883 | 402884 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr2 | 402883 | 403874 | a | 0 | ... | | chr4 | 402883 | 403874 | a | 0 | ... | | chr6 | 402883 | 403874 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain349-method_chain349] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain331-method_chain331] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 133 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain369-method_chain369] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2315007 | 2319930 | a | 0 | + | | | chr1 | 9287952 | 9288632 | a | 0 | + | | | chr1 | 8436291 | 8437848 | a | 0 | - | | | chr1 | 9950799 | 9959315 | a | 0 | - | | | chr13 | 7008715 | 7014764 | a | 0 | + | | | chr14 | 1129932 | 1133795 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 196904 | 203561 | a | 0 | + | | | chr1 | 3588 | 10245 | a | 0 | - | | | chr8 | 3588 | 10245 | a | 0 | + | | | chr8 | 3588 | 10245 | a | 0 | + | | | chr13 | 3588 | 10245 | a | 0 | - | | | chr14 | 3588 | 10245 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr11 | 722189 | 726805 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 180 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicpc+xSsNQGAXg89+b/7+QtpakrcWAYmkx5SopJNqhpUUUXISC7lVwEPQVuoi66qbiIHQQXHwBxSdQZ0d9BsHBRTFKh+5y1sPhfLxTup6VAQCDxmD7yujq8fme+HYY8Uzh8hALTELIKqMQ5FxxaF5UnRzVNLykakYcT1MIwoRePrhfCVCsbn43EAtvXLz0DDq6bdgazarndZ6a1N9/f+wiRM0J3k5fPz8eTu7yKGHXWtuvfxVaGc5WViP4Rq9JUSsnvs1PJqKmhdaTdvJcHgZqjisUMmx8FC9GZ+omR5iS9L8DEP+Hkw6Me4DWr0ejawBhKouMe+BxRogsufLnSTtbIw8DbpqRB+mSb5BexA9iqjhw') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 160 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 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Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 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('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain350-method_chain350] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 122 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain362-method_chain362] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain332-method_chain332] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain370-method_chain370] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 258 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAAkYGBGCEcpHFsAAAAQ0ABg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain351-method_chain351] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 108 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain364-method_chain364] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 167 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4AadQAVwQAADYAAY=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 269 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2AAA0Y4AafAAAAAVgAE') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain333-method_chain333] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 133 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain352-method_chain352] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain371-method_chain371] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 244 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain378-method_chain378] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 127 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain334-method_chain334] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E (and 26 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 131074 | 131075 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 272126 | 272127 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 272126 | 272128 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 272126 | 272128 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 272126 | 272128 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 272126 | 272128 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 272126 | 272128 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 272126 | 272128 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 272126 | 272127 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2555137 | 2555139 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain365-method_chain365] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 7122587 | 7130190 | a | 0 | + | | | chr1 | 7122587 | 7131982 | a | 0 | - | | | chr1 | 6779308 | 6786557 | a | 0 | - | | | chr11 | 5760411 | 5763480 | a | 0 | + | | | chr22 | 7122587 | 7123686 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5042109 | 5042191 | a | 0 | - | | | chr16 | 5042109 | 5042422 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 9469973 | 9476856 | a | 0 | + | | | chr4 | 405194 | 409478 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RlTNdn9L3wqntflw+zSwSb5uEy6fmBV/TDXrLEnjRn3T1bkCGcj80zvO4wgxwbKxs7MwMXIwujCCsjIx8rOxMjP6M8LwODKIMYk2564WoBZom3MQ/Cn85iMMlZN4uD0UllEy9zAPcfDkZZZjlGLjaGChYvDhY22U0MgTIBUswMHIyM0kyMfMwyTIxMnMyMbMwSLAzsrEzsDIwMzF57bgeFd39kdeH/bg/kM/BzMHADKQaGwPV37vi838PCwMNowcrAz8DFEMjMCJRhZOW3RFIIRMxAmMSmd5KdUXZCgwgDK2OW3WKdYqlHbIycjOwMkgK7GThBBgIAQr0wGg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 154 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain372-method_chain372] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain379-method_chain379] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E (and 116 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain335-method_chain335] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66306 | 66307 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8463848 | 8464105 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkAAI+IAYxmBjAgJGZkYEXRDPG6P68B5QBQa5G1ecgIaA4AENkBCM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain388-method_chain388] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 227115 | 229523 | a | 0 | - | E | chr1 | 1528426 | 1533018 | a | 0 | - | E | chr12 | 227115 | 233567 | a | 0 | - | E | chr14 | 227115 | 230511 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr16 | 227115 | 227628 | a | 0 | - | E | chr16 | 66563 | 70719 | a | 0 | - | E | chr20 | 227115 | 228404 | a | 0 | - | E | chr22 | 227115 | 231980 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 8 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 697402 | 702267 | a | 0 | + | E | chr1 | 227115 | 231546 | a | 0 | + | E | chr1 | 853794 | 858128 | a | 0 | - | E | chr1 | 143120 | 145528 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr14 | 918296 | 921692 | a | 0 | + | E | chr16 | 227115 | 227628 | a | 0 | - | E | chr16 | 2231560 | 2235716 | a | 0 | - | E | chr20 | 227115 | 228404 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1706759 | 1715977 | a | 0 | - | E | chr1 | 1179905 | 1189123 | a | 0 | - | E | chr1 | 1179905 | 1182722 | a | 0 | - | E | chr1 | 1179905 | 1189123 | a | 0 | - | E | chr1 | 22 | 9240 | a | 0 | - | E | chr1 | 1179905 | 1189123 | a | 0 | - | E | chr1 | 533254 | 542472 | a | 0 | - | E | chr1 | 2034986 | 2044204 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'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') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain374-method_chain374] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4609 | 5122 | a | 0 | + | E | chr1 | 4609 | 5122 | a | 0 | - | E | chr2 | 4609 | 5122 | a | 0 | + | E | chr17 | 4609 | 5122 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1797 | 9095 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 1794 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2fhn/vi3Z3GBa4PtrLUzphWz+S8N3t3azM/Ozuj1p7Dt3dIvbiy70PsFQkGRkZGJgYGARZmBkZBJkYGBmkGIQYGViYGIUYgB4iYmBl4GCCAnYWflyFPppGBFSjByMAEJhmB0iAWAzcDIxsDWAAAaboV1g==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1124664 | 1128995 | a | 0 | ... | | chr1 | 2100569 | 2105691 | a | 0 | ... | | chr16 | 5276744 | 5277513 | a | 0 | ... | | chr20 | 8383112 | 8383395 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain380-method_chain380] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7792641 | 7793981 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAAAAAABAAALAAMAATYyEt4AAAAAAQAndugAAABABTsAAQA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain336-method_chain336] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 176 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgYGFgZGQAAUYGCI0EGAEA8AAK') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain390-method_chain390] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain376-method_chain376] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'subtract'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAAUYgRABGRiyCcA6yIAABoQAK') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2803482 | 2803604 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2803482 | 2803604 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2803482 | 2803488 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain337-method_chain337] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain381-method_chain381] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1186817 | 1186819 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 196865 | 196867 | a | 0 | + | | | chr1 | 196865 | 197635 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | (and 57 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicJYxBCoBAEMOSrbiCePEm+Auf5+ddZ3sJTaF5EBqV82YfkGN2XN+CWzCN/o9GFobgipapgw89RgFN') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAI4AxkAAABSAAM=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain395-method_chain395] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain392-method_chain392] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 252 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain402-method_chain402] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain396-method_chain396] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 194 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain382-method_chain382] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain393-method_chain393] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 200 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain403-method_chain403] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain397-method_chain397] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 201 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain394-method_chain394] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain404-method_chain404] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 107 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain383-method_chain383] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 82070 | 86682 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 82070 | 86682 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1180417 | 1183746 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1180417 | 1183746 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1180417 | 1183746 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 82070 | 82596 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 82070 | 86682 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr22 | 1180417 | 1183746 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr22 | 1180417 | 1183746 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain398-method_chain398] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain405-method_chain405] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain384-method_chain384] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain411-method_chain411] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain399-method_chain399] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1176 E (and 122 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain406-method_chain406] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 251 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain400-method_chain400] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain385-method_chain385] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 269 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain413-method_chain413] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 167 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0Y4AaeQASNCEAAA4wAH') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 284 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgYGAEQgYwjUyBAQAAcgAF') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain407-method_chain407] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain401-method_chain401] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain386-method_chain386] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 134410 | 134411 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 154 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkYOAPKOB+wsgoY3mQh4ERCBkYmHg5GcCAEYUCAwB5KAMA') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain414-method_chain414] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 15146 | 15915 | a | 0 | + | | | chr1 | 15146 | 15915 | a | 0 | + | | | chr1 | 3515061 | 3515830 | a | 0 | + | | | chr1 | 6275263 | 6276032 | a | 0 | + | | | chr1 | 7441248 | 7441810 | a | 0 | - | | | chr1 | 1 | 1069 | a | 0 | - | | | chr1 | 330690 | 331459 | a | 0 | - | | | chr1 | 15146 | 15915 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 262150 | 262151 | a | 0 | + | | | chr1 | 327937 | 334176 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 18660 | 18662 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY4tMrVvFJnj5w0/GPatYzd+nntudd3onQ4mUgSVLnqDzTGYmx6VPWZKqD99hYdzxWaqo4AGbZrHoRQZeVkYGRh025vgD+5RZYrdsXX346dWTTJtvSLGYLtqiycbLys7KfdCMjZupioGBQZBJi02FTZbB+8Je3sLueD0mNTY2VgYbBmtNawZpE1YmQ2YmGRZtBhtmBlMmRjYmSWYGVgZGZSY2ZlZmRmZ2dkY2dhagdQwsTAyMLIxAlhQDiMHCwsDKAnQFUICVESjNwCARx87AyAdkMjIwg+wFMRgZPB5DaAYAOg8tcg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2555910 | 2556679 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 160 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AAAAAQ4AJgYGBQAAAAEAAAAAAAABAB4nAAUAAAMAAAA=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 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'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain415-method_chain415] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 196865 | 198402 | a | 0 | - | E | chr5 | 196865 | 198402 | a | 0 | - | E | chr5 | 196865 | 198402 | a | 0 | - | E | chr5 | 196865 | 198402 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8745595 | 8745853 | a | 0 | + | E | chr1 | 8745595 | 8745853 | a | 0 | + | E | chr1 | 8745595 | 8745853 | a | 0 | + | E | chr1 | 6797902 | 6798160 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicYzWIfWjG4sLKz87IwMDIyMzAzs7EwMkM5LAwcIEoRjYgZmJjZBFhZGTjYmHi4WdmYFRgUASJMsqzArVwpO/y5WRmZuZklmRm8GwtqmLgYQRqBAI7TgZGHiANAFnRBtw=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain428-method_chain428] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 115 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain420-method_chain420] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr7 | 1 | 48 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 145 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BgSOdl4GVgYmBgYGaAADZ2CBNE6DGwAEkAFHEAzA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain416-method_chain416] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8321461 | 8326597 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 169 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY1RKYV3FwAiGOXU/twApThF+BgYGRv3UoleMDBgAWQgACM0F8Q==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain425-method_chain425] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'subtract'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1291726 | 1291806 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY+RnlGVgYGBkYBDeehZI+YPZYBFGKAsKEMJIAABsZgIc') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr12 | 2901820 | 2906610 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2901820 | 2901821 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2901820 | 2901821 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2901820 | 2901821 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain429-method_chain429] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain421-method_chain421] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131074 | 131331 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6108673 | 6109372 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkYGbkY2BgYGTMYQABRgYGJhDBCGJXQYX4Y80YGGKZdjEC2QArpALA') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain430-method_chain430] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain427-method_chain427] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 129 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain417-method_chain417] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2RgZGcAAkY4AafgNJgJ5wAAAnQAEA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain437-method_chain437] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2062 | 3857 | a | 0 | + | E | chr1 | 2062 | 3857 | a | 0 | + | E | chr1 | 2062 | 3857 | a | 0 | + | E | chr1 | 2062 | 3857 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr1 | 2062 | 3857 | a | 0 | - | E | chr1 | 2062 | 3857 | a | 0 | - | E | chr1 | 2062 | 3857 | a | 0 | - | E | chr1 | 2062 | 3857 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 11 | 5428 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4065025 | 4065286 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY7Fh3W/FpLJHU/pyv7h02z8WIVGDMNYKFWYBVk3HyItsViKNb5mqGBgYmLJO2cyZE5ox9+9W7kI7FqO9/yTqT9QxWvyNNefnZmLg5GQEKuLjYhZh3s7CwM7AwcvAYsPKzsTEwqDJzMjPzsjGx8DAyCDGysDCzMAIBIJsDCxAASagLgYuIFNGVIOBF8hmY2Gy/cfAzwFkMtqxA1WwM4LUMTAAAKNIGxA=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5704394 | 5712743 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain434-method_chain434] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 97 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges 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('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain418-method_chain418] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340, in from_call | result: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 181, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 99, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 87, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 63, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 90, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 65, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 849, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 832, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 883, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 166, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 256, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 182, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1772, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 501, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 119, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 138, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 102, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1635, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 513 | 514 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2564 | 7685 | a | 0 | + | | | chr1 | 2564 | 7685 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2TgZIABJgYGRiDFyJhvsoCdsRosxsggwsDFzAAkGRlBPEaoKkYAQ58CFA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1245724 | 1246593 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:380 | (and 23 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2DgZGBkgAB2RhiLgUGYSZqDQYU5hYGBEQAGxwDY') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 258 | 518 | a | 0 | ... | | chr1 | 258 | 518 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain431-method_chain431] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain439-method_chain439] __________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain435-method_chain435] __________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 25 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2AAA0YJEMHOgAEAAxIAIg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain432-method_chain432] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 119 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain419-method_chain419] __________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGOGBEYiMk4IIAAOMABw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_introns_single ______________________________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 def test_introns_single(): "Assert that our fast method of computing introns is the same as the slow, correct one in compute_introns_single" gr = pr.data.gencode_gtf()[["gene_id", "Feature"]] exons = gr[gr.Feature == "exon"].merge(by="gene_id") exons.Feature = "exon" exons = exons.df df = pd.concat([gr[gr.Feature == "gene"].df, exons], sort=False) print(df) for gid, gdf in df.groupby("gene_id"): print("-------" * 20) print(gid) print(gdf) print("gdf", len(gdf)) expected = compute_introns_single(gdf, by="gene") print("expected", len(expected)) > actual = pr.PyRanges(gdf).features.introns().df tests/test_genomicfeatures.py:174: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/genomicfeatures.py:254: in introns result = pyrange_apply(_introns2, by_gr, exons, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/genomicfeatures.py:567: in _introns2 starts, ends, ids = find_introns(genes.Start.values, genes.End.values, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' sorted_nearest/src/introns.pyx:12: ValueError ----------------------------- Captured stdout call ----------------------------- Chromosome gene_id Start End Strand Feature 0 chr1 ENSG00000223972.5 11868 14409 + gene 1 chr1 ENSG00000243485.5 29553 31109 + gene 2 chr1 ENSG00000284332.1 30365 30503 + gene 3 chr1 ENSG00000268020.3 52472 53312 + gene 4 chr1 ENSG00000240361.2 57597 64116 + gene .. ... ... ... ... ... ... 587 chr1 ENSG00000283040.1 876754 877234 - exon 588 chr1 ENSG00000283712.1 1312501 1312566 - exon 589 chr1 ENSG00000284372.1 1339649 1339708 - exon 590 chr1 ENSG00000284662.1 685678 686673 - exon 591 chr1 ENSG00000284733.1 450702 451697 - exon [711 rows x 6 columns] -------------------------------------------------------------------------------------------------------------------------------------------- ENSG00000078808.16 Chromosome gene_id Start End Strand Feature 101 chr1 ENSG00000078808.16 1216907 1232031 - gene 284 chr1 ENSG00000078808.16 1216907 1217804 - exon 285 chr1 ENSG00000078808.16 1218457 1221351 - exon 286 chr1 ENSG00000078808.16 1223243 1223357 - exon 287 chr1 ENSG00000078808.16 1223831 1223968 - exon 288 chr1 ENSG00000078808.16 1227271 1227319 - exon 289 chr1 ENSG00000078808.16 1228467 1228946 - exon 290 chr1 ENSG00000078808.16 1231891 1232031 - exon gdf 8 g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g Chromosome gene_id Start End Strand Feature 101 chr1 ENSG00000078808.16 1216907 1232031 - gene x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x Chromosome Start End gene_id Strand 0 chr1 1216907 1217804 ENSG00000078808.16 - 1 chr1 1218457 1221351 ENSG00000078808.16 - 2 chr1 1223243 1223357 ENSG00000078808.16 - 3 chr1 1223831 1223968 ENSG00000078808.16 - 4 chr1 1227271 1227319 ENSG00000078808.16 - 5 chr1 1228467 1228946 ENSG00000078808.16 - 6 chr1 1231891 1232031 ENSG00000078808.16 - expected 6 _______________________________ test_merge[True] _______________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strand = True @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:31: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:75: in test_merge result = gr.merge(strand=strand, count=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_merge( E strand=True, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdfvtgh0d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1148697 | 1158437 | a | 0 | + | | chr1 | 1148697 | 1157799 | a | 0 | - | | chr1 | 492634 | 501736 | a | 0 | - | | chrX | 1148697 | 1157799 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpso8mn9x_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 492634 501736 - 1 chr1 1148697 1157799 - 1 chr1 1148697 1158437 + 1 chrX 1148697 1157799 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 492634 501736 - 1 1 chr1 1148697 1157799 - 1 2 chr1 1148697 1158437 + 1 3 chrX 1148697 1157799 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 198147 | 200823 | a | 0 | + | | chr1 | 198147 | 198989 | a | 0 | - | | chr2 | 198147 | 203282 | a | 0 | + | | chr2 | 198147 | 198989 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 198147 | 198941 | a | 0 | + | | chr2 | 198147 | 205638 | a | 0 | + | | chr2 | 198147 | 205627 | a | 0 | - | | chr2 | 198147 | 202960 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpcnrcuf_s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 198147 198989 - 1 chr1 198147 200823 + 1 chr2 198147 205638 + 7 chr2 198147 205627 - 2 bedtools_df Chromosome Start End Strand Count 0 chr1 198147 198989 - 1 1 chr1 198147 200823 + 1 2 chr2 198147 205638 + 7 3 chr2 198147 205627 - 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1314327 | 1315943 | a | 0 | - | | chr1 | 2297096 | 2299772 | a | 0 | - | | chr2 | 1314327 | 1315100 | a | 0 | + | | chr2 | 1314327 | 1316898 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 1314327 | 1319140 | a | 0 | - | | chr2 | 1314327 | 1317918 | a | 0 | - | | chr2 | 1314327 | 1315121 | a | 0 | - | | chr2 | 1314327 | 1317966 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpbp0gzayr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1314327 1315943 - 1 chr1 2297096 2299772 - 1 chr2 26 858 - 1 chr2 1314327 1319140 - 6 chr2 1314327 1316898 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1314327 1315943 - 1 1 chr1 2297096 2299772 - 1 2 chr2 26 858 - 1 3 chr2 1314327 1319140 - 6 4 chr2 1314327 1316898 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1314327 | 1317663 | a | 0 | + | | chr1 | 2297096 | 2299772 | a | 0 | + | | chr2 | 1314327 | 1317914 | a | 0 | + | | chr2 | 26 | 1368 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 1314327 | 1315105 | a | 0 | + | | chr2 | 1314327 | 1319140 | a | 0 | + | | chr2 | 1314327 | 1321502 | a | 0 | + | | chr2 | 1314327 | 1317925 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmps4n1x8br/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1314327 1317663 + 1 chr1 2297096 2299772 + 1 chr2 26 1368 + 1 chr2 1314327 1324313 + 7 bedtools_df Chromosome Start End Strand Count 0 chr1 1314327 1317663 + 1 1 chr1 2297096 2299772 + 1 2 chr2 26 1368 + 1 3 chr2 1314327 1324313 + 7 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1314327 | 1317663 | a | 0 | + | | chr1 | 2297096 | 2299772 | a | 0 | + | | chr2 | 1314327 | 1317914 | a | 0 | + | | chr2 | 26 | 1368 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 1314327 | 1315105 | a | 0 | + | | chr2 | 1314327 | 1319140 | a | 0 | + | | chr2 | 1314327 | 1321502 | a | 0 | + | | chr2 | 1314327 | 1317925 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpor81eh5d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1314327 1317663 + 1 chr1 2297096 2299772 + 1 chr2 26 1368 + 1 chr2 1314327 1324313 + 7 bedtools_df Chromosome Start End Strand Count 0 chr1 1314327 1317663 + 1 1 chr1 2297096 2299772 + 1 2 chr2 26 1368 + 1 3 chr2 1314327 1324313 + 7 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 198917 | 202253 | a | 0 | + | | chr1 | 2297096 | 2299772 | a | 0 | + | | chr2 | 198917 | 202504 | a | 0 | + | | chr2 | 26 | 1368 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 198917 | 199695 | a | 0 | + | | chr2 | 198917 | 203730 | a | 0 | + | | chr2 | 198917 | 206092 | a | 0 | + | | chr2 | 198917 | 202515 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdc8faotx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 198917 202253 + 1 chr1 2297096 2299772 + 1 chr2 26 1368 + 1 chr2 198917 208903 + 7 bedtools_df Chromosome Start End Strand Count 0 chr1 198917 202253 + 1 1 chr1 2297096 2299772 + 1 2 chr2 26 1368 + 1 3 chr2 198917 208903 + 7 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 198917 | 199175 | a | 0 | - | | chr1 | 2297096 | 2306070 | a | 0 | - | | chr2 | 198917 | 199175 | a | 0 | - | | chr2 | 26 | 1819 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 198917 | 199175 | a | 0 | - | | chr2 | 198917 | 199175 | a | 0 | - | | chr2 | 198917 | 199175 | a | 0 | - | | chr2 | 198917 | 199175 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_lnwebt6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 198917 199175 - 1 chr1 2297096 2306070 - 1 chr2 26 1819 - 1 chr2 198917 199175 - 7 bedtools_df Chromosome Start End Strand Count 0 chr1 198917 199175 - 1 1 chr1 2297096 2306070 - 1 2 chr2 26 1819 - 1 3 chr2 198917 199175 - 7 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4155965 | 4159805 | a | 0 | + | | chr1 | 4708821 | 4713523 | a | 0 | - | | chr1 | 1994678 | 1996147 | a | 0 | - | | chr1 | 3315189 | 3316225 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpmm9ouudz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1994678 1996147 - 1 chr1 3315189 3316225 - 1 chr1 4155965 4159805 + 1 chr1 4708821 4713523 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1994678 1996147 - 1 1 chr1 3315189 3316225 - 1 2 chr1 4155965 4159805 + 1 3 chr1 4708821 4713523 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65793 | 66052 | a | 0 | + | | chr1 | 65793 | 65899 | a | 0 | + | | chr1 | 65793 | 66563 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpikvwn_wd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 65793 66052 + 2 chr1 65793 66563 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 65793 66052 + 2 1 chr1 65793 66563 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpgc7wgogm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1h8rbety/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpig6u3308/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpg4cuugb0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphyk4a772/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpbzp0ncos/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdesydcfl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpmlat9jhf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmppp6kz7vy/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmptsbw_897/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpkemvgopi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpzq3jpnwu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2740708 | 2742767 | a | 0 | + | | chr1 | 6320661 | 6329951 | a | 0 | + | | chr1 | 7906809 | 7908248 | a | 0 | - | | chr1 | 8401424 | 8410136 | a | 0 | - | | chr1 | 3567880 | 3574998 | a | 0 | - | | chr7 | 5356824 | 5366416 | a | 0 | - | | chr17 | 5894515 | 5897963 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvn8stfn7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2740708 2742767 + 1 chr1 3567880 3574998 - 1 chr1 6320661 6329951 + 1 chr1 7906809 7908248 - 1 chr1 8401424 8410136 - 1 chr17 5894515 5897963 - 1 chr7 5356824 5366416 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2740708 2742767 + 1 1 chr1 3567880 3574998 - 1 2 chr1 6320661 6329951 + 1 3 chr1 7906809 7908248 - 1 4 chr1 8401424 8410136 - 1 5 chr17 5894515 5897963 - 1 6 chr7 5356824 5366416 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9408062 | 9416417 | a | 0 | + | | chr1 | 7733706 | 7743630 | a | 0 | + | | chr1 | 3713298 | 3713299 | a | 0 | - | | chr13 | 5978189 | 5982768 | a | 0 | - | | chr14 | 3940150 | 3940426 | a | 0 | + | | chr14 | 6215978 | 6225125 | a | 0 | - | | chr14 | 6489921 | 6494972 | a | 0 | - | | chrY | 6712926 | 6718145 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4_x90ezi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3713298 3713299 - 1 chr1 7733706 7743630 + 1 chr1 9408062 9416417 + 1 chr13 5978189 5982768 - 1 chr14 3940150 3940426 + 1 chr14 6215978 6225125 - 1 chr14 6489921 6494972 - 1 chrY 6712926 6718145 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3713298 3713299 - 1 1 chr1 7733706 7743630 + 1 2 chr1 9408062 9416417 + 1 3 chr13 5978189 5982768 - 1 4 chr14 3940150 3940426 + 1 5 chr14 6215978 6225125 - 1 6 chr14 6489921 6494972 - 1 7 chrY 6712926 6718145 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 2012678 | 2013674 | a | 0 | + | | chr6 | 9475471 | 9476467 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmprez4mlbd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr5 2012678 2013674 + 1 chr6 9475471 9476467 + 1 bedtools_df Chromosome Start End Strand Count 0 chr5 2012678 2013674 + 1 1 chr6 9475471 9476467 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 552879 | 561007 | a | 0 | + | | chr1 | 552879 | 557067 | a | 0 | - | | chr1 | 5443383 | 5444839 | a | 0 | - | | chr3 | 5813650 | 5821223 | a | 0 | + | | chr14 | 6604609 | 6612182 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpm2_18_ex/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 552879 557067 - 1 chr1 552879 561007 + 1 chr1 5443383 5444839 - 1 chr14 6604609 6612182 - 1 chr3 5813650 5821223 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 552879 557067 - 1 1 chr1 552879 561007 + 1 2 chr1 5443383 5444839 - 1 3 chr14 6604609 6612182 - 1 4 chr3 5813650 5821223 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1046903 | 1049664 | a | 0 | + | | chr1 | 5645534 | 5649633 | a | 0 | + | | chr1 | 6430858 | 6434957 | a | 0 | - | | chr1 | 557289 | 564104 | a | 0 | - | | chr10 | 7579911 | 7581028 | a | 0 | + | | chr13 | 6430858 | 6440612 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp67wq3rj7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 557289 564104 - 1 chr1 1046903 1049664 + 1 chr1 5645534 5649633 + 1 chr1 6430858 6434957 - 1 chr10 7579911 7581028 + 1 chr13 6430858 6440612 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 557289 564104 - 1 1 chr1 1046903 1049664 + 1 2 chr1 5645534 5649633 + 1 3 chr1 6430858 6434957 - 1 4 chr10 7579911 7581028 + 1 5 chr13 6430858 6440612 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7867 | a | 0 | + | | chr1 | 6955052 | 6959146 | a | 0 | - | | chr3 | 8570190 | 8574284 | a | 0 | - | | chr5 | 8296983 | 8301077 | a | 0 | + | | chr9 | 10000000 | 10004094 | a | 0 | + | | chr20 | 1209676 | 1213770 | a | 0 | - | | chr22 | 863374 | 871817 | a | 0 | + | | chrX | 9670884 | 9674978 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpla28rud9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7867 + 1 chr1 6955052 6959146 - 1 chr20 1209676 1213770 - 1 chr22 863374 871817 + 1 chr3 8570190 8574284 - 1 chr5 8296983 8301077 + 1 chr9 10000000 10004094 + 1 chrX 9670884 9674978 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 7867 + 1 1 chr1 6955052 6959146 - 1 2 chr20 1209676 1213770 - 1 3 chr22 863374 871817 + 1 4 chr3 8570190 8574284 - 1 5 chr5 8296983 8301077 + 1 6 chr9 10000000 10004094 + 1 7 chrX 9670884 9674978 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 3940580 | 3941905 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz_8apac6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr11 3940580 3941905 + 1 bedtools_df Chromosome Start End Strand Count 0 chr11 3940580 3941905 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8005095 | 8005640 | a | 0 | - | | chr5 | 4614853 | 4622915 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7ge4ghrs/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8005095 8005640 - 1 chr5 4614853 4622915 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8005095 8005640 - 1 1 chr5 4614853 4622915 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9497959 | 9507904 | a | 0 | + | | chr14 | 5490111 | 5499258 | a | 0 | - | | chr19 | 8272654 | 8273160 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpd1rdo93q/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9497959 9507904 + 1 chr14 5490111 5499258 - 1 chr19 8272654 8273160 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9497959 9507904 + 1 1 chr14 5490111 5499258 - 1 2 chr19 8272654 8273160 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5217280 | 5220914 | a | 0 | - | | chr1 | 8553912 | 8554850 | a | 0 | - | | chr1 | 4768594 | 4775364 | a | 0 | - | | chr1 | 10000000 | 10006442 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 3073621 | 3075787 | a | 0 | - | | chr17 | 8075460 | 8078661 | a | 0 | + | | chr21 | 1206524 | 1210789 | a | 0 | - | | chrY | 1465208 | 1465926 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpqptx8om7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4768594 4775364 - 1 chr1 5217280 5220914 - 1 chr1 8553912 8554850 - 1 chr1 10000000 10006442 - 1 chr14 3073621 3075787 - 1 chr17 8075460 8078661 + 1 chr2 9729403 9735704 - 1 chr21 1206524 1210789 - 1 chr5 1909252 1910737 + 1 chr5 3014387 3015184 + 1 chrY 1465208 1465926 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4768594 4775364 - 1 1 chr1 5217280 5220914 - 1 2 chr1 8553912 8554850 - 1 3 chr1 10000000 10006442 - 1 4 chr14 3073621 3075787 - 1 5 chr17 8075460 8078661 + 1 6 chr2 9729403 9735704 - 1 7 chr21 1206524 1210789 - 1 8 chr5 1909252 1910737 + 1 9 chr5 3014387 3015184 + 1 10 chrY 1465208 1465926 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2136498 | 2142769 | a | 0 | + | | chr1 | 2121949 | 2128165 | a | 0 | - | | chr1 | 5293899 | 5296562 | a | 0 | - | | chr1 | 5293899 | 5297664 | a | 0 | - | | chr13 | 3710200 | 3713361 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp73bsdj78/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2121949 2128165 - 1 chr1 2136498 2142769 + 1 chr1 5293899 5297664 - 2 chr13 3710200 3713361 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2121949 2128165 - 1 1 chr1 2136498 2142769 + 1 2 chr1 5293899 5297664 - 2 3 chr13 3710200 3713361 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2290695 | 2292777 | a | 0 | + | | chr1 | 5255660 | 5255661 | a | 0 | - | | chr11 | 3773631 | 3782932 | a | 0 | - | | chr21 | 3918427 | 3923969 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3le2257w/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2290695 2292777 + 1 chr1 5255660 5255661 - 1 chr11 3773631 3782932 - 1 chr21 3918427 3923969 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2290695 2292777 + 1 1 chr1 5255660 5255661 - 1 2 chr11 3773631 3782932 - 1 3 chr21 3918427 3923969 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6081795 | 6086200 | a | 0 | + | | chr1 | 5562118 | 5569020 | a | 0 | - | | chr1 | 6721848 | 6731848 | a | 0 | - | | chr6 | 6290414 | 6291185 | a | 0 | + | | chr12 | 6290414 | 6290859 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpaco87ov0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5562118 5569020 - 1 chr1 6081795 6086200 + 1 chr1 6721848 6731848 - 1 chr12 6290414 6290859 - 1 chr6 6290414 6291185 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5562118 5569020 - 1 1 chr1 6081795 6086200 + 1 2 chr1 6721848 6731848 - 1 3 chr12 6290414 6290859 - 1 4 chr6 6290414 6291185 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3631141 | 3636290 | a | 0 | + | | chr1 | 1981525 | 1987157 | a | 0 | + | | chr1 | 186238 | 192293 | a | 0 | + | | chr4 | 2 | 307 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrX | 9862710 | 9872709 | a | 0 | + | | chrX | 3768654 | 3775999 | a | 0 | - | | chrX | 1666923 | 1671398 | a | 0 | - | | chrX | 10000000 | 10002772 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1r0bwiqa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 186238 192293 + 1 chr1 1981525 1987157 + 1 chr1 3631141 3636290 + 1 chr14 6698152 6707682 - 1 chr15 3771111 3773068 + 1 chr4 2 307 + 1 chr7 9561301 9567387 - 1 chrX 1666923 1671398 - 1 chrX 3768654 3775999 - 1 chrX 9862710 9872709 + 1 chrX 10000000 10002772 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 186238 192293 + 1 1 chr1 1981525 1987157 + 1 2 chr1 3631141 3636290 + 1 3 chr14 6698152 6707682 - 1 4 chr15 3771111 3773068 + 1 5 chr4 2 307 + 1 6 chr7 9561301 9567387 - 1 7 chrX 1666923 1671398 - 1 8 chrX 3768654 3775999 - 1 9 chrX 9862710 9872709 + 1 10 chrX 10000000 10002772 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8517792 | 8522346 | a | 0 | + | | chr1 | 6324041 | 6333175 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphz8p7mlh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6324041 6333175 - 1 chr1 8517792 8522346 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6324041 6333175 - 1 1 chr1 8517792 8522346 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5410603 | 5412139 | a | 0 | - | | chr1 | 6424922 | 6426458 | a | 0 | - | | chr1 | 6550708 | 6552244 | a | 0 | - | | chr8 | 4282066 | 4283602 | a | 0 | - | | chr8 | 1569508 | 1571044 | a | 0 | - | | chr13 | 1656736 | 1658272 | a | 0 | + | | chr18 | 8233926 | 8236613 | a | 0 | + | | chr21 | 2495856 | 2497392 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_ou03f0k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5410603 5412139 - 1 chr1 6424922 6426458 - 1 chr1 6550708 6552244 - 1 chr13 1656736 1658272 + 1 chr18 8233926 8236613 + 1 chr21 2495856 2497392 + 1 chr8 1569508 1571044 - 1 chr8 4282066 4283602 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5410603 5412139 - 1 1 chr1 6424922 6426458 - 1 2 chr1 6550708 6552244 - 1 3 chr13 1656736 1658272 + 1 4 chr18 8233926 8236613 + 1 5 chr21 2495856 2497392 + 1 6 chr8 1569508 1571044 - 1 7 chr8 4282066 4283602 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3837404 | 3843627 | a | 0 | + | | chr1 | 9670299 | 9676522 | a | 0 | + | | chr1 | 4887244 | 4893467 | a | 0 | + | | chr1 | 8988603 | 8994826 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 4887244 | 4893467 | a | 0 | + | | chr1 | 8988603 | 8994826 | a | 0 | + | | chr1 | 1 | 1699 | a | 0 | + | | chr1 | 4560900 | 4563279 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp11j3meb4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 1699 + 1 chr1 3837404 3843627 + 1 chr1 4560900 4563279 - 1 chr1 4887244 4893467 + 1 chr1 8988603 8994826 + 1 chr1 9670299 9676522 + 1 chr12 9091909 9098132 - 1 chr20 1656842 1663834 - 1 chr20 4245907 4251214 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 1699 + 1 1 chr1 3837404 3843627 + 1 2 chr1 4560900 4563279 - 1 3 chr1 4887244 4893467 + 1 4 chr1 8988603 8994826 + 1 5 chr1 9670299 9676522 + 1 6 chr12 9091909 9098132 - 1 7 chr20 1656842 1663834 - 1 8 chr20 4245907 4251214 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1759541 | 1763280 | a | 0 | - | | chr18 | 8935393 | 8944235 | a | 0 | + | | chr19 | 2202407 | 2206249 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpspov23az/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1759541 1763280 - 1 chr18 8935393 8944235 + 1 chr19 2202407 2206249 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1759541 1763280 - 1 1 chr18 8935393 8944235 + 1 2 chr19 2202407 2206249 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9075420 | 9083673 | a | 0 | - | | chr1 | 1301444 | 1311208 | a | 0 | - | | chr1 | 7259485 | 7263223 | a | 0 | - | | chr1 | 9980420 | 9981816 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr6 | 5136187 | 5139925 | a | 0 | - | | chr7 | 7651083 | 7651789 | a | 0 | - | | chr20 | 7673569 | 7676969 | a | 0 | - | | chrY | 5168710 | 5172433 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7u9gy3xn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1301444 1311208 - 1 chr1 5987316 5988004 - 1 chr1 7259485 7263223 - 1 chr1 8508405 8514326 - 1 chr1 9075420 9083673 - 1 chr1 9980420 9981816 - 1 chr20 7673569 7676969 - 1 chr6 5136187 5139925 - 1 chr7 7651083 7651789 - 1 chrY 5168710 5172433 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1301444 1311208 - 1 1 chr1 5987316 5988004 - 1 2 chr1 7259485 7263223 - 1 3 chr1 8508405 8514326 - 1 4 chr1 9075420 9083673 - 1 5 chr1 9980420 9981816 - 1 6 chr20 7673569 7676969 - 1 7 chr6 5136187 5139925 - 1 8 chr7 7651083 7651789 - 1 9 chrY 5168710 5172433 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 4693106 | 4693108 | a | 0 | + | | chr11 | 5774128 | 5775054 | a | 0 | + | | chr11 | 157810 | 163545 | a | 0 | + | | chr11 | 8789733 | 8798223 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 8095225 | 8097147 | a | 0 | - | | chr11 | 6517179 | 6519599 | a | 0 | - | | chr11 | 4033876 | 4036922 | a | 0 | - | | chr11 | 3525137 | 3529415 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp9rnfdgv6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr11 157810 163545 + 1 chr11 1417725 1424339 - 1 chr11 3525137 3529415 - 1 chr11 4033876 4036922 - 1 chr11 4693106 4693108 + 1 chr11 5774128 5775054 + 1 chr11 6069693 6073466 - 1 chr11 6517179 6519599 - 1 chr11 6684334 6692366 - 1 chr11 8095225 8097147 - 1 chr11 8789733 8798223 - 1 bedtools_df Chromosome Start End Strand Count 0 chr11 157810 163545 + 1 1 chr11 1417725 1424339 - 1 2 chr11 3525137 3529415 - 1 3 chr11 4033876 4036922 - 1 4 chr11 4693106 4693108 + 1 5 chr11 5774128 5775054 + 1 6 chr11 6069693 6073466 - 1 7 chr11 6517179 6519599 - 1 8 chr11 6684334 6692366 - 1 9 chr11 8095225 8097147 - 1 10 chr11 8789733 8798223 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7502500 | 7505477 | a | 0 | + | | chr17 | 4812979 | 4812980 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpfiwuv7vp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7502500 7505477 + 1 chr17 4812979 4812980 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7502500 7505477 + 1 1 chr17 4812979 4812980 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 4457844 | 4465335 | a | 0 | + | | chr7 | 9137982 | 9137983 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3v7z556r/f1.bed) resultresultresultresultresultresultresultresultresultresult chr3 4457844 4465335 + 1 chr7 9137982 9137983 - 1 bedtools_df Chromosome Start End Strand Count 0 chr3 4457844 4465335 + 1 1 chr7 9137982 9137983 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 742443 | 749174 | a | 0 | + | | chr1 | 4241121 | 4247055 | a | 0 | - | | chr6 | 9122153 | 9128689 | a | 0 | + | | chr11 | 7578606 | 7578720 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpjatf4qda/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 742443 749174 + 1 chr1 4241121 4247055 - 1 chr11 7578606 7578720 - 1 chr6 9122153 9128689 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 742443 749174 + 1 1 chr1 4241121 4247055 - 1 2 chr11 7578606 7578720 - 1 3 chr6 9122153 9128689 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 4124488 | 4128576 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpayn983xk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 4124488 4128576 - 1 bedtools_df Chromosome Start End Strand Count 0 chr10 4124488 4128576 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8830965 | 8832010 | a | 0 | + | | chr1 | 4775539 | 4779428 | a | 0 | + | | chr1 | 6409469 | 6413416 | a | 0 | - | | chr1 | 7281043 | 7285161 | a | 0 | - | | chr22 | 6409469 | 6411031 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp5lhoof69/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4775539 4779428 + 1 chr1 6409469 6413416 - 1 chr1 7281043 7285161 - 1 chr1 8830965 8832010 + 1 chr22 6409469 6411031 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4775539 4779428 + 1 1 chr1 6409469 6413416 - 1 2 chr1 7281043 7285161 - 1 3 chr1 8830965 8832010 + 1 4 chr22 6409469 6411031 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5308975 | 5314222 | a | 0 | + | | chr1 | 9908842 | 9912123 | a | 0 | + | | chr1 | 6478780 | 6479661 | a | 0 | + | | chr1 | 8716132 | 8721533 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 5267653 | 5275986 | a | 0 | - | | chr9 | 6288888 | 6289231 | a | 0 | + | | chr10 | 1414139 | 1422152 | a | 0 | - | | chr16 | 6247446 | 6256634 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpy18u1alt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1589252 1596611 - 1 chr1 5308975 5314222 + 1 chr1 5998835 6003180 - 1 chr1 6478780 6479661 + 1 chr1 8716132 8721533 - 1 chr1 9270341 9277887 - 1 chr1 9908842 9912123 + 1 chr10 1414139 1422152 - 1 chr16 6247446 6256634 + 1 chr5 5267653 5275986 - 1 chr9 6288888 6289231 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1589252 1596611 - 1 1 chr1 5308975 5314222 + 1 2 chr1 5998835 6003180 - 1 3 chr1 6478780 6479661 + 1 4 chr1 8716132 8721533 - 1 5 chr1 9270341 9277887 - 1 6 chr1 9908842 9912123 + 1 7 chr10 1414139 1422152 - 1 8 chr16 6247446 6256634 + 1 9 chr5 5267653 5275986 - 1 10 chr9 6288888 6289231 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5092563 | 5095092 | a | 0 | + | | chr1 | 4793761 | 4800687 | a | 0 | + | | chr1 | 9771432 | 9774750 | a | 0 | + | | chr1 | 7051642 | 7060163 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 7051642 | 7060163 | a | 0 | - | | chr1 | 5239281 | 5244922 | a | 0 | - | | chr1 | 4898134 | 4900640 | a | 0 | - | | chr1 | 1014117 | 1016274 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp__xbpfzt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1014117 1016274 - 1 chr1 4793761 4800687 + 1 chr1 4898134 4900640 - 1 chr1 5092563 5095092 + 1 chr1 5239281 5244922 - 1 chr1 7051642 7060163 - 1 chr1 9771432 9774750 + 1 chr15 574941 576653 + 1 chr2 933064 942055 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1014117 1016274 - 1 1 chr1 4793761 4800687 + 1 2 chr1 4898134 4900640 - 1 3 chr1 5092563 5095092 + 1 4 chr1 5239281 5244922 - 1 5 chr1 7051642 7060163 - 1 6 chr1 9771432 9774750 + 1 7 chr15 574941 576653 + 1 8 chr2 933064 942055 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9060423 | 9065024 | a | 0 | + | | chr1 | 9481443 | 9486289 | a | 0 | + | | chr1 | 18252 | 20302 | a | 0 | - | | chr9 | 5815878 | 5819639 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpml8jbg4i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 18252 20302 - 1 chr1 9060423 9065024 + 1 chr1 9481443 9486289 + 1 chr9 5815878 5819639 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 18252 20302 - 1 1 chr1 9060423 9065024 + 1 2 chr1 9481443 9486289 + 1 3 chr9 5815878 5819639 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4818513 | 4821371 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_32mxuq2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4818513 4821371 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4818513 4821371 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2797852 | 2800042 | a | 0 | + | | chr1 | 1749658 | 1759604 | a | 0 | + | | chr1 | 6594699 | 6597136 | a | 0 | + | | chr1 | 8771783 | 8779861 | a | 0 | + | | chr1 | 5016188 | 5020187 | a | 0 | + | | chr1 | 1509064 | 1516631 | a | 0 | - | | chr9 | 861058 | 866604 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpidpksgcq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1509064 1516631 - 1 chr1 1749658 1759604 + 1 chr1 2797852 2800042 + 1 chr1 5016188 5020187 + 1 chr1 6594699 6597136 + 1 chr1 8771783 8779861 + 1 chr9 861058 866604 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1509064 1516631 - 1 1 chr1 1749658 1759604 + 1 2 chr1 2797852 2800042 + 1 3 chr1 5016188 5020187 + 1 4 chr1 6594699 6597136 + 1 5 chr1 8771783 8779861 + 1 6 chr9 861058 866604 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5647807 | 5647808 | a | 0 | + | | chr1 | 2608694 | 2615892 | a | 0 | + | | chr1 | 1543919 | 1553918 | a | 0 | + | | chr1 | 8060041 | 8069458 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 9716998 | 9726997 | a | 0 | - | | chr1 | 3728660 | 3731000 | a | 0 | - | | chr1 | 7105923 | 7109771 | a | 0 | - | | chr1 | 8488539 | 8498006 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmptf9leflk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 387875 387876 - 1 chr1 1543919 1553918 + 1 chr1 2608694 2615892 + 1 chr1 3728660 3731000 - 1 chr1 5647807 5647808 + 1 chr1 7105923 7109771 - 1 chr1 8060041 8069458 - 1 chr1 8488539 8498006 - 1 chr1 9716998 9726997 - 1 chr8 9773197 9778269 - 1 chr9 8965992 8965993 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 387875 387876 - 1 1 chr1 1543919 1553918 + 1 2 chr1 2608694 2615892 + 1 3 chr1 3728660 3731000 - 1 4 chr1 5647807 5647808 + 1 5 chr1 7105923 7109771 - 1 6 chr1 8060041 8069458 - 1 7 chr1 8488539 8498006 - 1 8 chr1 9716998 9726997 - 1 9 chr8 9773197 9778269 - 1 10 chr9 8965992 8965993 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr22 | 5655959 | 5665933 | a | 0 | + | | chr22 | 1 | 8948 | a | 0 | - | | chr22 | 5655959 | 5659273 | a | 0 | - | | chr22 | 2 | 8405 | a | 0 | - | | chr22 | 443036 | 446721 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvbr6kl2z/f1.bed) resultresultresultresultresultresultresultresultresultresult chr22 1 8948 - 2 chr22 443036 446721 - 1 chr22 5655959 5659273 - 1 chr22 5655959 5665933 + 1 bedtools_df Chromosome Start End Strand Count 0 chr22 1 8948 - 2 1 chr22 443036 446721 - 1 2 chr22 5655959 5659273 - 1 3 chr22 5655959 5665933 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3779437 | 3783920 | a | 0 | + | | chr10 | 2913993 | 2914249 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1j0hgwtm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3779437 3783920 + 1 chr10 2913993 2914249 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3779437 3783920 + 1 1 chr10 2913993 2914249 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6225284 | 6227733 | a | 0 | + | | chr1 | 6225284 | 6230952 | a | 0 | + | | chr1 | 6225284 | 6225786 | a | 0 | + | | chr1 | 6225284 | 6226961 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 6225284 | 6225923 | a | 0 | - | | chr5 | 6225284 | 6225786 | a | 0 | - | | chr10 | 6225284 | 6225786 | a | 0 | - | | chr18 | 6225284 | 6225786 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphbhe16es/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6225284 6230952 + 4 chr1 6225284 6229413 - 3 chr10 6225284 6225786 - 1 chr18 6225284 6225786 + 1 chr5 6225284 6225923 - 2 bedtools_df Chromosome Start End Strand Count 0 chr1 6225284 6230952 + 4 1 chr1 6225284 6229413 - 3 2 chr10 6225284 6225786 - 1 3 chr18 6225284 6225786 + 1 4 chr5 6225284 6225923 - 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 7436391 | 7436510 | a | 0 | - | | chrY | 3687626 | 3693469 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpk6xw12ho/f1.bed) resultresultresultresultresultresultresultresultresultresult chr9 7436391 7436510 - 1 chrY 3687626 3693469 + 1 bedtools_df Chromosome Start End Strand Count 0 chr9 7436391 7436510 - 1 1 chrY 3687626 3693469 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1925851 | 1928730 | a | 0 | + | | chr1 | 6250180 | 6253059 | a | 0 | + | | chr1 | 9496767 | 9497643 | a | 0 | - | | chr1 | 1339317 | 1342196 | a | 0 | - | | chr16 | 6956442 | 6959321 | a | 0 | - | | chr17 | 8004849 | 8007728 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpcf9zbi9n/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1339317 1342196 - 1 chr1 1925851 1928730 + 1 chr1 6250180 6253059 + 1 chr1 9496767 9497643 - 1 chr16 6956442 6959321 - 1 chr17 8004849 8007728 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1339317 1342196 - 1 1 chr1 1925851 1928730 + 1 2 chr1 6250180 6253059 + 1 3 chr1 9496767 9497643 - 1 4 chr16 6956442 6959321 - 1 5 chr17 8004849 8007728 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 6119178 | 6129178 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpg61wxoe8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr15 6119178 6129178 - 1 bedtools_df Chromosome Start End Strand Count 0 chr15 6119178 6129178 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 532434 | 538902 | a | 0 | - | | chr12 | 8072403 | 8075331 | a | 0 | - | | chr12 | 5428382 | 5438142 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpsr14czlr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr12 5428382 5438142 - 1 chr12 8072403 8075331 - 1 chr4 532434 538902 - 1 bedtools_df Chromosome Start End Strand Count 0 chr12 5428382 5438142 - 1 1 chr12 8072403 8075331 - 1 2 chr4 532434 538902 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4070657 | 4078528 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpsj_3vjql/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4070657 4078528 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4070657 4078528 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9351355 | 9359337 | a | 0 | + | | chr1 | 2011145 | 2020317 | a | 0 | + | | chr1 | 9999999 | 10008801 | a | 0 | + | | chr1 | 5203139 | 5205739 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 3323892 | 3324557 | a | 0 | - | | chr11 | 3488865 | 3492891 | a | 0 | + | | chr15 | 139737 | 141262 | a | 0 | + | | chr20 | 5213633 | 5220052 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpw9fpyysp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2011145 2020317 + 1 chr1 5203139 5205739 - 1 chr1 9351355 9359337 + 1 chr1 9626347 9627206 - 1 chr1 9999999 10008801 + 1 chr11 3488865 3492891 + 1 chr15 139737 141262 + 1 chr20 5213633 5220052 - 1 chr6 630411 630748 + 1 chr6 1577910 1579998 - 1 chr9 3323892 3324557 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2011145 2020317 + 1 1 chr1 5203139 5205739 - 1 2 chr1 9351355 9359337 + 1 3 chr1 9626347 9627206 - 1 4 chr1 9999999 10008801 + 1 5 chr11 3488865 3492891 + 1 6 chr15 139737 141262 + 1 7 chr20 5213633 5220052 - 1 8 chr6 630411 630748 + 1 9 chr6 1577910 1579998 - 1 10 chr9 3323892 3324557 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2001163 | 2010520 | a | 0 | + | | chr1 | 846950 | 848785 | a | 0 | + | | chr1 | 9856260 | 9856261 | a | 0 | + | | chr1 | 6314712 | 6324667 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1330230 | 1339634 | a | 0 | - | | chr1 | 6314712 | 6318751 | a | 0 | - | | chr1 | 6717379 | 6724681 | a | 0 | - | | chr1 | 3681591 | 3690687 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvux7f9iv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 846950 848785 + 1 chr1 1330230 1339634 - 1 chr1 2001163 2010520 + 1 chr1 3681591 3690687 - 1 chr1 6314712 6318751 - 1 chr1 6314712 6324667 + 1 chr1 6717379 6724681 - 1 chr1 9856260 9856261 + 1 chr21 10000000 10000217 - 1 chr3 413779 418414 + 1 chr4 1668065 1676269 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 846950 848785 + 1 1 chr1 1330230 1339634 - 1 2 chr1 2001163 2010520 + 1 3 chr1 3681591 3690687 - 1 4 chr1 6314712 6318751 - 1 5 chr1 6314712 6324667 + 1 6 chr1 6717379 6724681 - 1 7 chr1 9856260 9856261 + 1 8 chr21 10000000 10000217 - 1 9 chr3 413779 418414 + 1 10 chr4 1668065 1676269 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 4048384 | 4049492 | a | 0 | - | | chr20 | 6952418 | 6956339 | a | 0 | + | | chr20 | 1050846 | 1059744 | a | 0 | - | | chrX | 170336 | 174357 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpyhw2xxy1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr20 1050846 1059744 - 1 chr20 6952418 6956339 + 1 chr8 4048384 4049492 - 1 chrX 170336 174357 - 1 bedtools_df Chromosome Start End Strand Count 0 chr20 1050846 1059744 - 1 1 chr20 6952418 6956339 + 1 2 chr8 4048384 4049492 - 1 3 chrX 170336 174357 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 8430047 | 8431232 | a | 0 | - | | chr20 | 2080926 | 2088412 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmps6bej612/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 8430047 8431232 - 1 chr20 2080926 2088412 + 1 bedtools_df Chromosome Start End Strand Count 0 chr10 8430047 8431232 - 1 1 chr20 2080926 2088412 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7599463 | 7600592 | a | 0 | + | | chr1 | 107749 | 115206 | a | 0 | - | | chr1 | 9264170 | 9271400 | a | 0 | - | | chr2 | 389153 | 390500 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 8408148 | 8409538 | a | 0 | + | | chr4 | 3932590 | 3940047 | a | 0 | + | | chr4 | 1121763 | 1123909 | a | 0 | - | | chr20 | 7633023 | 7640480 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpbnuwaw87/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 107749 115206 - 1 chr1 7599463 7600592 + 1 chr1 9264170 9271400 - 1 chr2 389153 390500 + 1 chr20 7633023 7640480 - 1 chr22 6694120 6703123 + 1 chr3 8869086 8876507 - 1 chr4 1121763 1123909 - 1 chr4 3932590 3940047 + 1 chr4 8408148 8409538 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 107749 115206 - 1 1 chr1 7599463 7600592 + 1 2 chr1 9264170 9271400 - 1 3 chr2 389153 390500 + 1 4 chr20 7633023 7640480 - 1 5 chr22 6694120 6703123 + 1 6 chr3 8869086 8876507 - 1 7 chr4 1121763 1123909 - 1 8 chr4 3932590 3940047 + 1 9 chr4 8408148 8409538 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 8844574 | 8853822 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmps5pp1d1a/f1.bed) resultresultresultresultresultresultresultresultresultresult chr7 8844574 8853822 - 1 bedtools_df Chromosome Start End Strand Count 0 chr7 8844574 8853822 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1058848 | 1063307 | a | 0 | + | | chr1 | 4179359 | 4182007 | a | 0 | + | | chr1 | 3014759 | 3024270 | a | 0 | + | | chr1 | 684901 | 694801 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 5402574 | 5403188 | a | 0 | + | | chr20 | 2564664 | 2573882 | a | 0 | + | | chr22 | 1641125 | 1646355 | a | 0 | + | | chrX | 1295170 | 1302674 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpc5yrhro9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 684901 694801 - 1 chr1 1058848 1063307 + 1 chr1 2976026 2983225 - 1 chr1 3014759 3024270 + 1 chr1 4179359 4182007 + 1 chr1 9045795 9054247 - 1 chr18 5402574 5403188 + 1 chr20 2564664 2573882 + 1 chr22 1641125 1646355 + 1 chr5 5654237 5662031 - 1 chrX 1295170 1302674 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 684901 694801 - 1 1 chr1 1058848 1063307 + 1 2 chr1 2976026 2983225 - 1 3 chr1 3014759 3024270 + 1 4 chr1 4179359 4182007 + 1 5 chr1 9045795 9054247 - 1 6 chr18 5402574 5403188 + 1 7 chr20 2564664 2573882 + 1 8 chr22 1641125 1646355 + 1 9 chr5 5654237 5662031 - 1 10 chrX 1295170 1302674 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9505779 | 9509768 | a | 0 | - | | chr1 | 7448507 | 7454774 | a | 0 | - | | chr8 | 4806764 | 4813090 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpglfwp9px/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7448507 7454774 - 1 chr1 9505779 9509768 - 1 chr8 4806764 4813090 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7448507 7454774 - 1 1 chr1 9505779 9509768 - 1 2 chr8 4806764 4813090 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8003712 | 8008310 | a | 0 | + | | chr1 | 10000000 | 10005158 | a | 0 | + | | chr1 | 2478397 | 2484680 | a | 0 | - | | chr1 | 7462888 | 7470575 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr17 | 1758852 | 1763967 | a | 0 | + | | chr18 | 289754 | 294912 | a | 0 | - | | chr21 | 2222579 | 2227650 | a | 0 | - | | chrM | 1657095 | 1661862 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmppd5up64i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2478397 2484680 - 1 chr1 3602748 3608153 - 1 chr1 7462888 7470575 - 1 chr1 8003712 8008310 + 1 chr1 8835100 8839774 - 1 chr1 10000000 10005158 + 1 chr17 1758852 1763967 + 1 chr18 289754 294912 - 1 chr21 2222579 2227650 - 1 chr8 9213959 9222238 + 1 chrM 1657095 1661862 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2478397 2484680 - 1 1 chr1 3602748 3608153 - 1 2 chr1 7462888 7470575 - 1 3 chr1 8003712 8008310 + 1 4 chr1 8835100 8839774 - 1 5 chr1 10000000 10005158 + 1 6 chr17 1758852 1763967 + 1 7 chr18 289754 294912 - 1 8 chr21 2222579 2227650 - 1 9 chr8 9213959 9222238 + 1 10 chrM 1657095 1661862 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5827942 | 5827943 | a | 0 | + | | chr1 | 5827942 | 5828323 | a | 0 | - | | chr4 | 5827942 | 5829679 | a | 0 | - | | chr5 | 5827942 | 5836113 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 5827942 | 5831566 | a | 0 | - | | chr18 | 5827942 | 5835370 | a | 0 | + | | chr22 | 5827942 | 5836500 | a | 0 | + | | chrM | 5827942 | 5828490 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 10 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1fqs5nbf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5827942 5827943 + 1 chr1 5827942 5828323 - 1 chr11 5827942 5835196 + 1 chr15 5827942 5834319 + 1 chr16 5827942 5831566 - 1 chr18 5827942 5835370 + 1 chr22 5827942 5836500 + 1 chr4 5827942 5829679 - 1 chr5 5827942 5836113 + 1 chr6 5827942 5836139 - 1 chrM 5827942 5828490 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5827942 5827943 + 1 1 chr1 5827942 5828323 - 1 2 chr11 5827942 5835196 + 1 3 chr15 5827942 5834319 + 1 4 chr16 5827942 5831566 - 1 5 chr18 5827942 5835370 + 1 6 chr22 5827942 5836500 + 1 7 chr4 5827942 5829679 - 1 8 chr5 5827942 5836113 + 1 9 chr6 5827942 5836139 - 1 10 chrM 5827942 5828490 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2533909 | 2534731 | a | 0 | + | | chr1 | 8512415 | 8522243 | a | 0 | - | | chr1 | 9498250 | 9499031 | a | 0 | - | | chr2 | 8774011 | 8779633 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 493900 | 499128 | a | 0 | - | | chr13 | 10000000 | 10000781 | a | 0 | - | | chr16 | 493900 | 503020 | a | 0 | - | | chr20 | 8949427 | 8950208 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpp_wrn_5_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2533909 2534731 + 1 chr1 8512415 8522243 - 1 chr1 9498250 9499031 - 1 chr13 493900 499128 - 1 chr13 10000000 10000781 - 1 chr16 493900 503020 - 1 chr2 5363263 5364044 - 1 chr2 8774011 8779633 - 1 chr20 8949427 8950208 + 1 chr9 493900 501963 - 1 chrM 9999999 10000780 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2533909 2534731 + 1 1 chr1 8512415 8522243 - 1 2 chr1 9498250 9499031 - 1 3 chr13 493900 499128 - 1 4 chr13 10000000 10000781 - 1 5 chr16 493900 503020 - 1 6 chr2 5363263 5364044 - 1 7 chr2 8774011 8779633 - 1 8 chr20 8949427 8950208 + 1 9 chr9 493900 501963 - 1 10 chrM 9999999 10000780 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2460093 | 2468304 | a | 0 | - | | chr1 | 9332747 | 9340627 | a | 0 | - | | chr1 | 7595797 | 7604224 | a | 0 | - | | chr9 | 4122876 | 4123688 | a | 0 | - | | chr19 | 2331103 | 2336590 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmph_ao5lyw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2460093 2468304 - 1 chr1 7595797 7604224 - 1 chr1 9332747 9340627 - 1 chr19 2331103 2336590 + 1 chr9 4122876 4123688 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2460093 2468304 - 1 1 chr1 7595797 7604224 - 1 2 chr1 9332747 9340627 - 1 3 chr19 2331103 2336590 + 1 4 chr9 4122876 4123688 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1683444 | 1684956 | a | 0 | + | | chr1 | 8428003 | 8435542 | a | 0 | - | | chr1 | 9351996 | 9359535 | a | 0 | - | | chr17 | 2268566 | 2276105 | a | 0 | + | | chr21 | 7443006 | 7447093 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdpbbf43x/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1683444 1684956 + 1 chr1 8428003 8435542 - 1 chr1 9351996 9359535 - 1 chr17 2268566 2276105 + 1 chr21 7443006 7447093 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1683444 1684956 + 1 1 chr1 8428003 8435542 - 1 2 chr1 9351996 9359535 - 1 3 chr17 2268566 2276105 + 1 4 chr21 7443006 7447093 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7074719 | 7080701 | a | 0 | + | | chr1 | 4067295 | 4073277 | a | 0 | - | | chr1 | 8251664 | 8257646 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_0l1cmgd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4067295 4073277 - 1 chr1 7074719 7080701 + 1 chr1 8251664 8257646 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4067295 4073277 - 1 1 chr1 7074719 7080701 + 1 2 chr1 8251664 8257646 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8478454 | 8479191 | a | 0 | - | | chr9 | 6150422 | 6151159 | a | 0 | + | | chr11 | 2152221 | 2160134 | a | 0 | + | | chr13 | 8478454 | 8479744 | a | 0 | + | | chrM | 8678864 | 8679601 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpq01m4m3e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8478454 8479191 - 1 chr11 2152221 2160134 + 1 chr13 8478454 8479744 + 1 chr9 6150422 6151159 + 1 chrM 8678864 8679601 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8478454 8479191 - 1 1 chr11 2152221 2160134 + 1 2 chr13 8478454 8479744 + 1 3 chr9 6150422 6151159 + 1 4 chrM 8678864 8679601 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 2 | 3811 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpejs0p0fk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr9 2 3811 + 1 bedtools_df Chromosome Start End Strand Count 0 chr9 2 3811 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3528856 | 3537453 | a | 0 | + | | chr1 | 1950510 | 1959107 | a | 0 | + | | chr1 | 5011518 | 5016296 | a | 0 | - | | chr1 | 9832078 | 9840675 | a | 0 | - | | chr3 | 2203723 | 2208108 | a | 0 | - | | chr15 | 4736523 | 4741428 | a | 0 | - | | chr16 | 3589162 | 3597759 | a | 0 | + | | chr22 | 5250707 | 5259304 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp81m19_hn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1950510 1959107 + 1 chr1 3528856 3537453 + 1 chr1 5011518 5016296 - 1 chr1 9832078 9840675 - 1 chr15 4736523 4741428 - 1 chr16 3589162 3597759 + 1 chr22 5250707 5259304 - 1 chr3 2203723 2208108 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1950510 1959107 + 1 1 chr1 3528856 3537453 + 1 2 chr1 5011518 5016296 - 1 3 chr1 9832078 9840675 - 1 4 chr15 4736523 4741428 - 1 5 chr16 3589162 3597759 + 1 6 chr22 5250707 5259304 - 1 7 chr3 2203723 2208108 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr22 | 2799966 | 2803811 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvn5iup7w/f1.bed) resultresultresultresultresultresultresultresultresultresult chr22 2799966 2803811 + 1 bedtools_df Chromosome Start End Strand Count 0 chr22 2799966 2803811 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 2468319 | 2476725 | a | 0 | + | | chr14 | 232957 | 241454 | a | 0 | + | | chr14 | 7924652 | 7934374 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_i80bqsz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr14 232957 241454 + 1 chr14 2468319 2476725 + 1 chr14 7924652 7934374 - 1 bedtools_df Chromosome Start End Strand Count 0 chr14 232957 241454 + 1 1 chr14 2468319 2476725 + 1 2 chr14 7924652 7934374 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 4039572 | 4040499 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpwr6qfui2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr14 4039572 4040499 + 1 bedtools_df Chromosome Start End Strand Count 0 chr14 4039572 4040499 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6069801 | 6077552 | a | 0 | + | | chr1 | 1771842 | 1777709 | a | 0 | - | | chr5 | 3728300 | 3730017 | a | 0 | - | | chr5 | 8599863 | 8599865 | a | 0 | - | | chr5 | 3565521 | 3572184 | a | 0 | - | | chr22 | 8293707 | 8297408 | a | 0 | + | | chrM | 5485860 | 5491650 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp8dirh2u4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1771842 1777709 - 1 chr1 6069801 6077552 + 1 chr22 8293707 8297408 + 1 chr5 3565521 3572184 - 1 chr5 3728300 3730017 - 1 chr5 8599863 8599865 - 1 chrM 5485860 5491650 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1771842 1777709 - 1 1 chr1 6069801 6077552 + 1 2 chr22 8293707 8297408 + 1 3 chr5 3565521 3572184 - 1 4 chr5 3728300 3730017 - 1 5 chr5 8599863 8599865 - 1 6 chrM 5485860 5491650 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1846139 | 1846225 | a | 0 | + | | chr1 | 1 | 9470 | a | 0 | + | | chr1 | 4943834 | 4951857 | a | 0 | - | | chr1 | 8603111 | 8603873 | a | 0 | - | | chr1 | 7491229 | 7498326 | a | 0 | - | | chr17 | 4574342 | 4583292 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpm8o4er5b/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 9470 + 1 chr1 1846139 1846225 + 1 chr1 4943834 4951857 - 1 chr1 7491229 7498326 - 1 chr1 8603111 8603873 - 1 chr17 4574342 4583292 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 9470 + 1 1 chr1 1846139 1846225 + 1 2 chr1 4943834 4951857 - 1 3 chr1 7491229 7498326 - 1 4 chr1 8603111 8603873 - 1 5 chr17 4574342 4583292 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9743443 | 9752382 | a | 0 | + | | chr1 | 5443780 | 5447742 | a | 0 | + | | chr1 | 4979413 | 4988911 | a | 0 | + | | chr1 | 1639967 | 1643229 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 21182 | 30990 | a | 0 | + | | chr10 | 8792468 | 8795512 | a | 0 | - | | chr12 | 2541628 | 2548936 | a | 0 | - | | chrM | 21182 | 28490 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz7njunkk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 341453 348761 - 1 chr1 1639967 1643229 + 1 chr1 3326239 3336106 + 1 chr1 4979413 4988911 + 1 chr1 5443780 5447742 + 1 chr1 9743443 9752382 + 1 chr1 9878808 9884448 + 1 chr10 8792468 8795512 - 1 chr12 2541628 2548936 - 1 chr4 21182 30990 + 1 chrM 21182 28490 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 341453 348761 - 1 1 chr1 1639967 1643229 + 1 2 chr1 3326239 3336106 + 1 3 chr1 4979413 4988911 + 1 4 chr1 5443780 5447742 + 1 5 chr1 9743443 9752382 + 1 6 chr1 9878808 9884448 + 1 7 chr10 8792468 8795512 - 1 8 chr12 2541628 2548936 - 1 9 chr4 21182 30990 + 1 10 chrM 21182 28490 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7288358 | 7288756 | a | 0 | + | | chr1 | 840005 | 840403 | a | 0 | + | | chr1 | 82598 | 82996 | a | 0 | - | | chr1 | 1311315 | 1311713 | a | 0 | - | | chr1 | 8273612 | 8274010 | a | 0 | - | | chr1 | 9460988 | 9461386 | a | 0 | - | | chrY | 4342655 | 4343053 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpw3ndlvcd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 82598 82996 - 1 chr1 840005 840403 + 1 chr1 1311315 1311713 - 1 chr1 7288358 7288756 + 1 chr1 8273612 8274010 - 1 chr1 9460988 9461386 - 1 chrY 4342655 4343053 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 82598 82996 - 1 1 chr1 840005 840403 + 1 2 chr1 1311315 1311713 - 1 3 chr1 7288358 7288756 + 1 4 chr1 8273612 8274010 - 1 5 chr1 9460988 9461386 - 1 6 chrY 4342655 4343053 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2987797 | 2997282 | a | 0 | + | | chr1 | 2987797 | 2991236 | a | 0 | + | | chr1 | 2987797 | 2990330 | a | 0 | + | | chr1 | 2987797 | 2991614 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 2987797 | 2990466 | a | 0 | + | | chr17 | 1241566 | 1241925 | a | 0 | - | | chr19 | 2987797 | 2990491 | a | 0 | - | | chrM | 2987797 | 2993227 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpk8te7l2k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2987797 2991614 - 2 chr1 2987797 2997282 + 3 chr13 2987797 2988698 - 1 chr14 2987797 2990466 + 1 chr17 1241566 1241925 - 1 chr19 2987797 2990491 - 1 chr5 2987797 2994294 - 1 chrM 2987797 2993227 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2987797 2991614 - 2 1 chr1 2987797 2997282 + 3 2 chr13 2987797 2988698 - 1 3 chr14 2987797 2990466 + 1 4 chr17 1241566 1241925 - 1 5 chr19 2987797 2990491 - 1 6 chr5 2987797 2994294 - 1 7 chrM 2987797 2993227 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 7437125 | 7444884 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpbjtixp4e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr15 7437125 7444884 + 1 bedtools_df Chromosome Start End Strand Count 0 chr15 7437125 7444884 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5001200 | 5007221 | a | 0 | + | | chr1 | 5001200 | 5004622 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvll38qvh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5001200 5004622 - 1 chr1 5001200 5007221 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5001200 5004622 - 1 1 chr1 5001200 5007221 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7269167 | 7275270 | a | 0 | + | | chr1 | 10000000 | 10004241 | a | 0 | + | | chr1 | 3318815 | 3325942 | a | 0 | - | | chr6 | 3931220 | 3935242 | a | 0 | - | | chr15 | 8247336 | 8257272 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmph9xk6xex/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3318815 3325942 - 1 chr1 7269167 7275270 + 1 chr1 10000000 10004241 + 1 chr15 8247336 8257272 - 1 chr6 3931220 3935242 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3318815 3325942 - 1 1 chr1 7269167 7275270 + 1 2 chr1 10000000 10004241 + 1 3 chr15 8247336 8257272 - 1 4 chr6 3931220 3935242 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2282145 | 2282328 | a | 0 | + | | chr1 | 9099749 | 9109195 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpjaqmd8br/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2282145 2282328 + 1 chr1 9099749 9109195 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2282145 2282328 + 1 1 chr1 9099749 9109195 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8956079 | 8959768 | a | 0 | + | | chr1 | 9305921 | 9315053 | a | 0 | + | | chr1 | 8698518 | 8707681 | a | 0 | + | | chr1 | 7847172 | 7848996 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr20 | 2892292 | 2892874 | a | 0 | + | | chr21 | 5246472 | 5251259 | a | 0 | + | | chr22 | 1709521 | 1715161 | a | 0 | + | | chrM | 5803432 | 5809650 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz1f_7ii_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4517166 4517795 + 1 chr1 6028101 6032170 - 1 chr1 7847172 7848996 + 1 chr1 8698518 8707681 + 1 chr1 8956079 8959768 + 1 chr1 9305921 9315053 + 1 chr17 8214113 8218912 + 1 chr20 2892292 2892874 + 1 chr21 5246472 5251259 + 1 chr22 1709521 1715161 + 1 chrM 5803432 5809650 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4517166 4517795 + 1 1 chr1 6028101 6032170 - 1 2 chr1 7847172 7848996 + 1 3 chr1 8698518 8707681 + 1 4 chr1 8956079 8959768 + 1 5 chr1 9305921 9315053 + 1 6 chr17 8214113 8218912 + 1 7 chr20 2892292 2892874 + 1 8 chr21 5246472 5251259 + 1 9 chr22 1709521 1715161 + 1 10 chrM 5803432 5809650 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2051625 | 2058683 | a | 0 | + | | chr1 | 5721442 | 5729645 | a | 0 | + | | chr1 | 3902883 | 3909552 | a | 0 | + | | chr1 | 7763561 | 7770687 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2759719 | 2765939 | a | 0 | + | | chr1 | 465378 | 473581 | a | 0 | - | | chr1 | 2570341 | 2578544 | a | 0 | - | | chr1 | 9848750 | 9856953 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp55ajqwef/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 465378 473581 - 1 chr1 2051625 2058683 + 1 chr1 2570341 2578544 - 1 chr1 2759719 2765939 + 1 chr1 3902883 3909552 + 1 chr1 5721442 5729645 + 1 chr1 7763561 7770687 + 1 chr1 9848750 9856953 - 1 chr10 5595315 5596864 - 1 chr6 8236138 8237189 + 1 chr9 10000000 10007508 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 465378 473581 - 1 1 chr1 2051625 2058683 + 1 2 chr1 2570341 2578544 - 1 3 chr1 2759719 2765939 + 1 4 chr1 3902883 3909552 + 1 5 chr1 5721442 5729645 + 1 6 chr1 7763561 7770687 + 1 7 chr1 9848750 9856953 - 1 8 chr10 5595315 5596864 - 1 9 chr6 8236138 8237189 + 1 10 chr9 10000000 10007508 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9037958 | 9039790 | a | 0 | - | | chr1 | 2289756 | 2293848 | a | 0 | - | | chr1 | 1 | 9450 | a | 0 | - | | chr1 | 5354102 | 5361196 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1728734 | 1731456 | a | 0 | - | | chr1 | 2857073 | 2857965 | a | 0 | - | | chr1 | 3334800 | 3340313 | a | 0 | - | | chr1 | 1 | 2735 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz5cishuq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 9450 - 2 chr1 1728734 1731456 - 1 chr1 1871809 1881258 - 1 chr1 2289756 2293848 - 1 chr1 2857073 2857965 - 1 chr1 3112114 3121563 - 1 chr1 3334800 3340313 - 1 chr1 5354102 5361196 - 1 chr1 9037958 9039790 - 1 chr5 9335143 9340462 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 9450 - 2 1 chr1 1728734 1731456 - 1 2 chr1 1871809 1881258 - 1 3 chr1 2289756 2293848 - 1 4 chr1 2857073 2857965 - 1 5 chr1 3112114 3121563 - 1 6 chr1 3334800 3340313 - 1 7 chr1 5354102 5361196 - 1 8 chr1 9037958 9039790 - 1 9 chr5 9335143 9340462 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7866178 | 7875417 | a | 0 | + | | chr1 | 5934471 | 5935932 | a | 0 | + | | chr1 | 9572507 | 9579014 | a | 0 | - | | chr3 | 1 | 1100 | a | 0 | - | | chr6 | 8393676 | 8396239 | a | 0 | - | | chr8 | 1 | 6249 | a | 0 | - | | chr13 | 153493 | 157917 | a | 0 | - | | chr14 | 4528391 | 4533233 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpwyvgcwry/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5934471 5935932 + 1 chr1 7866178 7875417 + 1 chr1 9572507 9579014 - 1 chr13 153493 157917 - 1 chr14 4528391 4533233 + 1 chr3 1 1100 - 1 chr6 8393676 8396239 - 1 chr8 1 6249 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5934471 5935932 + 1 1 chr1 7866178 7875417 + 1 2 chr1 9572507 9579014 - 1 3 chr13 153493 157917 - 1 4 chr14 4528391 4533233 + 1 5 chr3 1 1100 - 1 6 chr6 8393676 8396239 - 1 7 chr8 1 6249 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4629125 | 4634617 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphdhw1hnb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4629125 4634617 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4629125 4634617 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5490372 | 5499731 | a | 0 | + | | chr1 | 1 | 5349 | a | 0 | + | | chr1 | 7446046 | 7447973 | a | 0 | + | | chr1 | 10000000 | 10001927 | a | 0 | - | | chr1 | 5603652 | 5609852 | a | 0 | - | | chr1 | 9156605 | 9158532 | a | 0 | - | | chr16 | 1381922 | 1382413 | a | 0 | - | | chr18 | 9430150 | 9434726 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpuh3f9yj4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5349 + 1 chr1 5490372 5499731 + 1 chr1 5603652 5609852 - 1 chr1 7446046 7447973 + 1 chr1 9156605 9158532 - 1 chr1 10000000 10001927 - 1 chr16 1381922 1382413 - 1 chr18 9430150 9434726 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 5349 + 1 1 chr1 5490372 5499731 + 1 2 chr1 5603652 5609852 - 1 3 chr1 7446046 7447973 + 1 4 chr1 9156605 9158532 - 1 5 chr1 10000000 10001927 - 1 6 chr16 1381922 1382413 - 1 7 chr18 9430150 9434726 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9911878 | 9921752 | a | 0 | + | | chr2 | 6834905 | 6838895 | a | 0 | + | | chr6 | 5607946 | 5613278 | a | 0 | + | | chr18 | 5607946 | 5617117 | a | 0 | - | | chrY | 1991890 | 1994040 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp148abmrm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9911878 9921752 + 1 chr18 5607946 5617117 - 1 chr2 6834905 6838895 + 1 chr6 5607946 5613278 + 1 chrY 1991890 1994040 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9911878 9921752 + 1 1 chr18 5607946 5617117 - 1 2 chr2 6834905 6838895 + 1 3 chr6 5607946 5613278 + 1 4 chrY 1991890 1994040 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2326699 | 2336618 | a | 0 | + | | chr1 | 8185063 | 8192216 | a | 0 | + | | chr10 | 962952 | 965581 | a | 0 | - | | chr14 | 1069959 | 1077726 | a | 0 | - | | chr15 | 962952 | 965901 | a | 0 | + | | chr20 | 8935397 | 8937183 | a | 0 | + | | chr22 | 8300611 | 8303720 | a | 0 | + | | chr22 | 1237473 | 1238126 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp2e1lrq80/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2326699 2336618 + 1 chr1 8185063 8192216 + 1 chr10 962952 965581 - 1 chr14 1069959 1077726 - 1 chr15 962952 965901 + 1 chr20 8935397 8937183 + 1 chr22 1237473 1238126 + 1 chr22 8300611 8303720 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2326699 2336618 + 1 1 chr1 8185063 8192216 + 1 2 chr10 962952 965581 - 1 3 chr14 1069959 1077726 - 1 4 chr15 962952 965901 + 1 5 chr20 8935397 8937183 + 1 6 chr22 1237473 1238126 + 1 7 chr22 8300611 8303720 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8402687 | 8403162 | a | 0 | + | | chr1 | 226961 | 229195 | a | 0 | + | | chr1 | 8110409 | 8119601 | a | 0 | + | | chr1 | 9916664 | 9919421 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 2408411 | 2415547 | a | 0 | + | | chr15 | 3873439 | 3881239 | a | 0 | - | | chr16 | 8121363 | 8128135 | a | 0 | - | | chrX | 7728265 | 7731861 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpjdlfgxo_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 226961 229195 + 1 chr1 685014 686213 - 1 chr1 1410379 1417912 - 1 chr1 3686105 3687953 - 1 chr1 8110409 8119601 + 1 chr1 8402687 8403162 + 1 chr1 9916664 9919421 + 1 chr15 3873439 3881239 - 1 chr16 8121363 8128135 - 1 chr2 2408411 2415547 + 1 chrX 7728265 7731861 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 226961 229195 + 1 1 chr1 685014 686213 - 1 2 chr1 1410379 1417912 - 1 3 chr1 3686105 3687953 - 1 4 chr1 8110409 8119601 + 1 5 chr1 8402687 8403162 + 1 6 chr1 9916664 9919421 + 1 7 chr15 3873439 3881239 - 1 8 chr16 8121363 8128135 - 1 9 chr2 2408411 2415547 + 1 10 chrX 7728265 7731861 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1864237 | 1867859 | a | 0 | - | | chr1 | 1713988 | 1716326 | a | 0 | - | | chr1 | 130017 | 137422 | a | 0 | - | | chr1 | 3083267 | 3087857 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 5496 | 9807 | a | 0 | - | | chr20 | 6987916 | 6993878 | a | 0 | + | | chrX | 4585549 | 4590540 | a | 0 | + | | chrX | 47642 | 50988 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp2vtmw9g0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 130017 137422 - 1 chr1 1713988 1716326 - 1 chr1 1864237 1867859 - 1 chr1 3083267 3087857 - 1 chr1 4956756 4966332 - 1 chr11 8189394 8189396 - 1 chr18 5496 9807 - 1 chr20 6987916 6993878 + 1 chr8 4956756 4960007 - 1 chrX 47642 50988 - 1 chrX 4585549 4590540 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 130017 137422 - 1 1 chr1 1713988 1716326 - 1 2 chr1 1864237 1867859 - 1 3 chr1 3083267 3087857 - 1 4 chr1 4956756 4966332 - 1 5 chr11 8189394 8189396 - 1 6 chr18 5496 9807 - 1 7 chr20 6987916 6993878 + 1 8 chr8 4956756 4960007 - 1 9 chrX 47642 50988 - 1 10 chrX 4585549 4590540 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2408003 | 2415800 | a | 0 | + | | chr10 | 1 | 8712 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4nbr3ghp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2408003 2415800 + 1 chr10 1 8712 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2408003 2415800 + 1 1 chr10 1 8712 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8698265 | 8700566 | a | 0 | + | | chr10 | 7648417 | 7653348 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0d3z7s9b/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8698265 8700566 + 1 chr10 7648417 7653348 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8698265 8700566 + 1 1 chr10 7648417 7653348 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5583897 | 5587563 | a | 0 | + | | chr1 | 5583897 | 5591212 | a | 0 | + | | chr1 | 5583897 | 5593525 | a | 0 | + | | chr1 | 5583897 | 5589218 | a | 0 | - | | chr13 | 5583897 | 5588741 | a | 0 | + | | chr17 | 5583897 | 5592219 | a | 0 | + | | chrX | 5583897 | 5591432 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp5wjiuyn_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5583897 5593525 + 3 chr1 5583897 5589218 - 1 chr13 5583897 5588741 + 1 chr17 5583897 5592219 + 1 chrX 5583897 5591432 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5583897 5593525 + 3 1 chr1 5583897 5589218 - 1 2 chr13 5583897 5588741 + 1 3 chr17 5583897 5592219 + 1 4 chrX 5583897 5591432 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 9376002 | 9378377 | a | 0 | + | | chr13 | 2460430 | 2467082 | a | 0 | + | | chr18 | 4950691 | 4953066 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmph7o94e3c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 9376002 9378377 + 1 chr13 2460430 2467082 + 1 chr18 4950691 4953066 + 1 bedtools_df Chromosome Start End Strand Count 0 chr10 9376002 9378377 + 1 1 chr13 2460430 2467082 + 1 2 chr18 4950691 4953066 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 826674 | 834378 | a | 0 | + | | chr1 | 4997765 | 5007765 | a | 0 | + | | chr1 | 692928 | 700632 | a | 0 | + | | chr5 | 6754664 | 6758919 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 875258 | 878913 | a | 0 | - | | chr12 | 8641488 | 8643386 | a | 0 | - | | chr12 | 131128 | 138755 | a | 0 | - | | chr12 | 5357616 | 5363153 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpjlnx9k50/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 692928 700632 + 1 chr1 826674 834378 + 1 chr1 4997765 5007765 + 1 chr12 2 8740 + 1 chr12 131128 138755 - 1 chr12 875258 878913 - 1 chr12 5357616 5363153 - 1 chr12 8641488 8643386 - 1 chr12 9214429 9219763 + 1 chr17 8710202 8713701 + 1 chr5 6754664 6758919 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 692928 700632 + 1 1 chr1 826674 834378 + 1 2 chr1 4997765 5007765 + 1 3 chr12 2 8740 + 1 4 chr12 131128 138755 - 1 5 chr12 875258 878913 - 1 6 chr12 5357616 5363153 - 1 7 chr12 8641488 8643386 - 1 8 chr12 9214429 9219763 + 1 9 chr17 8710202 8713701 + 1 10 chr5 6754664 6758919 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9458181 | 9460296 | a | 0 | + | | chr1 | 5974095 | 5976210 | a | 0 | + | | chr1 | 7205031 | 7207146 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3m04hefz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5974095 5976210 + 1 chr1 7205031 7207146 - 1 chr1 9458181 9460296 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5974095 5976210 + 1 1 chr1 7205031 7207146 - 1 2 chr1 9458181 9460296 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 7993998 | 7995016 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp8m52e7vr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr15 7993998 7995016 - 1 bedtools_df Chromosome Start End Strand Count 0 chr15 7993998 7995016 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 6689237 | 6698689 | a | 0 | + | | chrY | 8817376 | 8824768 | a | 0 | + | | chrY | 3821590 | 3823445 | a | 0 | + | | chrY | 9129249 | 9134417 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chrY | 8073293 | 8075148 | a | 0 | - | | chrY | 6062489 | 6071840 | a | 0 | - | | chrY | 10000000 | 10008941 | a | 0 | - | | chrY | 3932823 | 3934678 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpy8wmg7c0/f1.bed) resultresultresultresultresultresultresultresultresultresult chrY 3821590 3823445 + 1 chrY 3932823 3934678 - 1 chrY 5341501 5347671 - 1 chrY 6062489 6071840 - 1 chrY 6689237 6698689 + 1 chrY 8073293 8075148 - 1 chrY 8817376 8824768 + 1 chrY 9129249 9134417 - 1 chrY 10000000 10008941 - 1 bedtools_df Chromosome Start End Strand Count 0 chrY 3821590 3823445 + 1 1 chrY 3932823 3934678 - 1 2 chrY 5341501 5347671 - 1 3 chrY 6062489 6071840 - 1 4 chrY 6689237 6698689 + 1 5 chrY 8073293 8075148 - 1 6 chrY 8817376 8824768 + 1 7 chrY 9129249 9134417 - 1 8 chrY 10000000 10008941 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9608020 | 9617934 | a | 0 | + | | chr1 | 2261546 | 2268113 | a | 0 | + | | chr1 | 6399205 | 6408995 | a | 0 | + | | chr1 | 8463784 | 8467452 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5968624 | 5978624 | a | 0 | - | | chr1 | 4358638 | 4363406 | a | 0 | - | | chr1 | 3671006 | 3677458 | a | 0 | - | | chr1 | 8856852 | 8860770 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpcnhavqi0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2261546 2268113 + 1 chr1 3671006 3677458 - 1 chr1 4358638 4363406 - 1 chr1 5968624 5978624 - 1 chr1 6399205 6408995 + 1 chr1 8463784 8467452 - 1 chr1 8856852 8860770 - 1 chr1 9608020 9617934 + 1 chr22 4476794 4481630 + 1 chr4 1676419 1681114 - 1 chr7 3798236 3801987 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2261546 2268113 + 1 1 chr1 3671006 3677458 - 1 2 chr1 4358638 4363406 - 1 3 chr1 5968624 5978624 - 1 4 chr1 6399205 6408995 + 1 5 chr1 8463784 8467452 - 1 6 chr1 8856852 8860770 - 1 7 chr1 9608020 9617934 + 1 8 chr22 4476794 4481630 + 1 9 chr4 1676419 1681114 - 1 10 chr7 3798236 3801987 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3467556 | 3470775 | a | 0 | - | | chr1 | 6528798 | 6535721 | a | 0 | - | | chr1 | 3467556 | 3473081 | a | 0 | - | | chr20 | 3467556 | 3473395 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpivv25q7t/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3467556 3473081 - 2 chr1 6528798 6535721 - 1 chr20 3467556 3473395 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3467556 3473081 - 2 1 chr1 6528798 6535721 - 1 2 chr20 3467556 3473395 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9122 | a | 0 | + | | chr1 | 7380578 | 7387942 | a | 0 | + | | chr1 | 5900149 | 5905145 | a | 0 | + | | chr1 | 8434017 | 8439986 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 5158798 | 5167569 | a | 0 | + | | chr7 | 6444901 | 6446517 | a | 0 | - | | chr19 | 9691503 | 9691719 | a | 0 | + | | chrX | 6264390 | 6272322 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpu57kz2vh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 9122 + 1 chr1 203009 212676 + 1 chr1 5900149 5905145 + 1 chr1 6092958 6102309 + 1 chr1 7380578 7387942 + 1 chr1 8434017 8439986 + 1 chr1 9523844 9530299 + 1 chr19 9691503 9691719 + 1 chr4 5158798 5167569 + 1 chr7 6444901 6446517 - 1 chrX 6264390 6272322 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 9122 + 1 1 chr1 203009 212676 + 1 2 chr1 5900149 5905145 + 1 3 chr1 6092958 6102309 + 1 4 chr1 7380578 7387942 + 1 5 chr1 8434017 8439986 + 1 6 chr1 9523844 9530299 + 1 7 chr19 9691503 9691719 + 1 8 chr4 5158798 5167569 + 1 9 chr7 6444901 6446517 - 1 10 chrX 6264390 6272322 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6015727 | 6022434 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1e8f1lab/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6015727 6022434 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6015727 6022434 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrX | 9297545 | 9300352 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpfeeyzjdf/f1.bed) resultresultresultresultresultresultresultresultresultresult chrX 9297545 9300352 - 1 bedtools_df Chromosome Start End Strand Count 0 chrX 9297545 9300352 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5103538 | 5113167 | a | 0 | + | | chr1 | 688095 | 689890 | a | 0 | - | | chr1 | 3788051 | 3789461 | a | 0 | - | | chr1 | 1477162 | 1484974 | a | 0 | - | | chr17 | 6369899 | 6371694 | a | 0 | + | | chr22 | 688095 | 689890 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmprxue86lh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 688095 689890 - 1 chr1 1477162 1484974 - 1 chr1 3788051 3789461 - 1 chr1 5103538 5113167 + 1 chr17 6369899 6371694 + 1 chr22 688095 689890 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 688095 689890 - 1 1 chr1 1477162 1484974 - 1 2 chr1 3788051 3789461 - 1 3 chr1 5103538 5113167 + 1 4 chr17 6369899 6371694 + 1 5 chr22 688095 689890 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4514005 | 4518610 | a | 0 | + | | chr1 | 1831124 | 1837220 | a | 0 | - | | chr6 | 1893006 | 1893613 | a | 0 | - | | chr10 | 9139342 | 9146614 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmph4pc8j3x/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1831124 1837220 - 1 chr1 4514005 4518610 + 1 chr10 9139342 9146614 - 1 chr6 1893006 1893613 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1831124 1837220 - 1 1 chr1 4514005 4518610 + 1 2 chr10 9139342 9146614 - 1 3 chr6 1893006 1893613 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1826407 | 1830718 | a | 0 | + | | chr1 | 4585114 | 4588147 | a | 0 | + | | chr1 | 6439108 | 6440706 | a | 0 | + | | chr1 | 1826407 | 1835195 | a | 0 | + | | chr1 | 9213845 | 9215455 | a | 0 | + | | chr1 | 1826407 | 1830425 | a | 0 | - | | chr9 | 3447140 | 3454050 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpxw2m7r56/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1826407 1830425 - 1 chr1 1826407 1835195 + 2 chr1 4585114 4588147 + 1 chr1 6439108 6440706 + 1 chr1 9213845 9215455 + 1 chr9 3447140 3454050 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1826407 1830425 - 1 1 chr1 1826407 1835195 + 2 2 chr1 4585114 4588147 + 1 3 chr1 6439108 6440706 + 1 4 chr1 9213845 9215455 + 1 5 chr9 3447140 3454050 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1427239 | 1431087 | a | 0 | + | | chr1 | 7796701 | 7805722 | a | 0 | - | | chr7 | 5854999 | 5864999 | a | 0 | - | | chr14 | 3318053 | 3318618 | a | 0 | - | | chr17 | 2408168 | 2416912 | a | 0 | + | | chr17 | 9376301 | 9385944 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpcbzmz15m/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1427239 1431087 + 1 chr1 7796701 7805722 - 1 chr14 3318053 3318618 - 1 chr17 2408168 2416912 + 1 chr17 9376301 9385944 - 1 chr7 5854999 5864999 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1427239 1431087 + 1 1 chr1 7796701 7805722 - 1 2 chr14 3318053 3318618 - 1 3 chr17 2408168 2416912 + 1 4 chr17 9376301 9385944 - 1 5 chr7 5854999 5864999 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8764303 | 8770927 | a | 0 | + | | chr1 | 5366798 | 5369432 | a | 0 | + | | chr1 | 5164321 | 5171734 | a | 0 | - | | chr1 | 9574856 | 9579683 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 9674561 | 9675781 | a | 0 | - | | chr1 | 9933808 | 9942266 | a | 0 | - | | chr1 | 5004292 | 5009119 | a | 0 | - | | chr1 | 3330995 | 3334351 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp9h45dkea/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2712009 2719877 - 1 chr1 3330995 3334351 - 1 chr1 3959164 3963991 - 1 chr1 5004292 5009119 - 1 chr1 5164321 5171734 - 1 chr1 5366798 5369432 + 1 chr1 8764303 8770927 + 1 chr1 9574856 9579683 - 1 chr1 9674561 9675781 - 1 chr1 9933808 9942266 - 1 chr11 698951 701500 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2712009 2719877 - 1 1 chr1 3330995 3334351 - 1 2 chr1 3959164 3963991 - 1 3 chr1 5004292 5009119 - 1 4 chr1 5164321 5171734 - 1 5 chr1 5366798 5369432 + 1 6 chr1 8764303 8770927 + 1 7 chr1 9574856 9579683 - 1 8 chr1 9674561 9675781 - 1 9 chr1 9933808 9942266 - 1 10 chr11 698951 701500 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3828540 | 3829539 | a | 0 | + | | chr1 | 3828540 | 3829085 | a | 0 | + | | chr1 | 1067401 | 1067717 | a | 0 | + | | chr1 | 6206853 | 6212237 | a | 0 | - | | chr1 | 1459285 | 1464817 | a | 0 | - | | chr4 | 3364320 | 3367946 | a | 0 | - | | chr4 | 3828540 | 3829539 | a | 0 | - | | chr18 | 3828540 | 3832799 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphybrvtm2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1067401 1067717 + 1 chr1 1459285 1464817 - 1 chr1 3828540 3829539 + 2 chr1 6206853 6212237 - 1 chr18 3828540 3832799 - 1 chr4 3364320 3367946 - 1 chr4 3828540 3829539 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1067401 1067717 + 1 1 chr1 1459285 1464817 - 1 2 chr1 3828540 3829539 + 2 3 chr1 6206853 6212237 - 1 4 chr18 3828540 3832799 - 1 5 chr4 3364320 3367946 - 1 6 chr4 3828540 3829539 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 6246967 | 6248018 | a | 0 | - | | chr18 | 8148868 | 8153306 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpc7bpmkby/f1.bed) resultresultresultresultresultresultresultresultresultresult chr13 6246967 6248018 - 1 chr18 8148868 8153306 - 1 bedtools_df Chromosome Start End Strand Count 0 chr13 6246967 6248018 - 1 1 chr18 8148868 8153306 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5583418 | 5592486 | a | 0 | + | | chr1 | 7923647 | 7929096 | a | 0 | + | | chr1 | 2166566 | 2175366 | a | 0 | + | | chr1 | 5987465 | 5992488 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 5583418 | 5592486 | a | 0 | + | | chr1 | 9945951 | 9947796 | a | 0 | + | | chr1 | 5903925 | 5911038 | a | 0 | - | | chr1 | 5583418 | 5592486 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpfg4t9gjq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2166566 2175366 + 1 chr1 5583418 5592486 + 2 chr1 5583418 5592486 - 1 chr1 5903925 5911038 - 1 chr1 5987465 5992488 + 1 chr1 7923647 7929096 + 1 chr1 9945951 9947796 + 1 chr16 4935364 4940020 - 1 chr16 5583418 5588353 + 1 chr18 5583418 5592486 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2166566 2175366 + 1 1 chr1 5583418 5592486 + 2 2 chr1 5583418 5592486 - 1 3 chr1 5903925 5911038 - 1 4 chr1 5987465 5992488 + 1 5 chr1 7923647 7929096 + 1 6 chr1 9945951 9947796 + 1 7 chr16 4935364 4940020 - 1 8 chr16 5583418 5588353 + 1 9 chr18 5583418 5592486 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3365593 | 3374159 | a | 0 | + | | chr1 | 180675 | 186261 | a | 0 | - | | chr1 | 5259963 | 5268529 | a | 0 | - | | chr2 | 7511941 | 7519071 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr10 | 3365593 | 3373262 | a | 0 | + | | chr10 | 218764 | 226294 | a | 0 | + | | chr16 | 4474823 | 4483389 | a | 0 | - | | chr21 | 3365593 | 3366641 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpe00hhr4j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 180675 186261 - 1 chr1 3365593 3374159 + 1 chr1 5259963 5268529 - 1 chr10 218764 226294 + 1 chr10 3365593 3373262 + 1 chr16 4474823 4483389 - 1 chr2 3365593 3374159 - 2 chr2 7511941 7519071 - 1 chr21 3365593 3366641 - 1 chr7 7190451 7198794 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 180675 186261 - 1 1 chr1 3365593 3374159 + 1 2 chr1 5259963 5268529 - 1 3 chr10 218764 226294 + 1 4 chr10 3365593 3373262 + 1 5 chr16 4474823 4483389 - 1 6 chr2 3365593 3374159 - 2 7 chr2 7511941 7519071 - 1 8 chr21 3365593 3366641 - 1 9 chr7 7190451 7198794 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpwz_9d36s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 ______________________________ test_cluster[True] ______________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strand = True @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:132: in test_cluster result = gr.cluster(strand=strand) pyranges/pyranges.py:1070: in cluster df = pyrange_apply_single(_cluster, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/cluster.py:14: in _cluster ids = annotate_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_cluster( E strand=True, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/annotate_clusters.pyx:15: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpfny28whk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 378393 | 382466 | a | 0 | + | | chr1 | 1328072 | 1334534 | a | 0 | + | | chr1 | 6952762 | 6956835 | a | 0 | + | | chr1 | 350281 | 354354 | a | 0 | - | | chr1 | 5358871 | 5364699 | a | 0 | - | | chr1 | 2177174 | 2181247 | a | 0 | - | | chr7 | 2177174 | 2181247 | a | 0 | - | | chrX | 7872229 | 7878172 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp3jlflvi2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 378393 382466 a 0 + 1 1 chr1 1328072 1334534 a 0 + 2 2 chr1 6952762 6956835 a 0 + 3 3 chr1 350281 354354 a 0 - 4 4 chr1 2177174 2181247 a 0 - 5 5 chr1 5358871 5364699 a 0 - 6 6 chr7 2177174 2181247 a 0 - 7 7 chrX 7872229 7878172 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 378393 | 382466 | a | 0 | + | | chr1 | 1328072 | 1334534 | a | 0 | + | | chr1 | 6952762 | 6956835 | a | 0 | + | | chr1 | 350281 | 354354 | a | 0 | - | | chr1 | 5358871 | 5364699 | a | 0 | - | | chr1 | 2177174 | 2181247 | a | 0 | - | | chr7 | 2177174 | 2181247 | a | 0 | - | | chrX | 7872229 | 7878172 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 378393 | 382466 | a | 0 | + | | chr1 | 1328072 | 1334534 | a | 0 | + | | chr1 | 6952762 | 6956835 | a | 0 | + | | chr1 | 350281 | 354354 | a | 0 | - | | chr1 | 5358871 | 5364699 | a | 0 | - | | chr1 | 2177174 | 2181247 | a | 0 | - | | chr7 | 2177174 | 2181247 | a | 0 | + | | chrX | 7872229 | 7878172 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpkkyv78ae/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 378393 382466 a 0 + 1 1 chr1 1328072 1334534 a 0 + 2 2 chr1 6952762 6956835 a 0 + 3 3 chr1 350281 354354 a 0 - 4 4 chr1 2177174 2181247 a 0 - 5 5 chr1 5358871 5364699 a 0 - 6 6 chr7 2177174 2181247 a 0 + 7 7 chrX 7872229 7878172 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 378393 | 382466 | a | 0 | + | | chr1 | 1328072 | 1334534 | a | 0 | + | | chr1 | 6952762 | 6956835 | a | 0 | + | | chr1 | 350281 | 354354 | a | 0 | - | | chr1 | 5358871 | 5364699 | a | 0 | - | | chr1 | 2177174 | 2181247 | a | 0 | - | | chr7 | 2177174 | 2181247 | a | 0 | + | | chrX | 7872229 | 7878172 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6312390 | 6318852 | a | 0 | + | | chr1 | 6952762 | 6953337 | a | 0 | + | | chr1 | 131607 | 140112 | a | 0 | + | | chr1 | 1585927 | 1591755 | a | 0 | + | | chr1 | 6686041 | 6690114 | a | 0 | - | | chr1 | 23 | 4096 | a | 0 | - | | chr1 | 4441888 | 4447831 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpbtb4ddzn/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 131607 140112 a 0 + 1 1 chr1 1585927 1591755 a 0 + 2 2 chr1 6312390 6318852 a 0 + 3 3 chr1 6952762 6953337 a 0 + 4 4 chr1 23 4096 a 0 - 5 5 chr1 4441888 4447831 a 0 - 6 6 chr1 6686041 6690114 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6312390 | 6318852 | a | 0 | + | | chr1 | 6952762 | 6953337 | a | 0 | + | | chr1 | 131607 | 140112 | a | 0 | + | | chr1 | 1585927 | 1591755 | a | 0 | + | | chr1 | 6686041 | 6690114 | a | 0 | - | | chr1 | 23 | 4096 | a | 0 | - | | chr1 | 4441888 | 4447831 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6312390 | 6318852 | a | 0 | + | | chr1 | 6952762 | 6953337 | a | 0 | + | | chr1 | 131607 | 140112 | a | 0 | + | | chr1 | 1585927 | 1591755 | a | 0 | + | | chr1 | 6686041 | 6690114 | a | 0 | - | | chr1 | 23 | 4096 | a | 0 | - | | chr1 | 4441888 | 4447831 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpaqzelbm7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 131607 140112 a 0 + 1 1 chr1 1585927 1591755 a 0 + 2 2 chr1 6312390 6318852 a 0 + 3 3 chr1 6952762 6953337 a 0 + 4 4 chr1 23 4096 a 0 - 5 5 chr1 4441888 4447831 a 0 - 6 6 chr1 6686041 6690114 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6312390 | 6318852 | a | 0 | + | | chr1 | 6952762 | 6953337 | a | 0 | + | | chr1 | 131607 | 140112 | a | 0 | + | | chr1 | 1585927 | 1591755 | a | 0 | + | | chr1 | 6686041 | 6690114 | a | 0 | - | | chr1 | 23 | 4096 | a | 0 | - | | chr1 | 4441888 | 4447831 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | - | | chr1 | 66310 | 66568 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmfgzdms7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 66310 66568 a 0 + 1 1 chr1 66310 66568 a 0 + 1 2 chr1 66310 66568 a 0 + 1 3 chr1 66310 66568 a 0 + 1 4 chr1 66310 66568 a 0 - 2 5 chr1 66310 66568 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | - | | chr1 | 66310 | 66568 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | - | | chr1 | 66310 | 66568 | a | 0 | - | | chr2 | 66310 | 66568 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp0h6u3u45/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 66310 66568 a 0 + 1 1 chr1 66310 66568 a 0 + 1 2 chr1 66310 66568 a 0 + 1 3 chr1 66310 66568 a 0 - 2 4 chr1 66310 66568 a 0 - 2 5 chr2 66310 66568 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | + | | chr1 | 66310 | 66568 | a | 0 | - | | chr1 | 66310 | 66568 | a | 0 | - | | chr2 | 66310 | 66568 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1443332 | 1444637 | a | 0 | + | | chr1 | 459010 | 460323 | a | 0 | + | | chr1 | 459010 | 460323 | a | 0 | + | | chr1 | 1282 | 2595 | a | 0 | + | | chr1 | 459010 | 466695 | a | 0 | + | | chr1 | 65794 | 67331 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp19emuoru/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1282 2595 a 0 + 1 1 chr1 65794 67331 a 0 + 2 2 chr1 459010 460323 a 0 + 3 3 chr1 459010 460323 a 0 + 3 4 chr1 459010 466695 a 0 + 3 5 chr1 1443332 1444637 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1443332 | 1444637 | a | 0 | + | | chr1 | 459010 | 460323 | a | 0 | + | | chr1 | 459010 | 460323 | a | 0 | + | | chr1 | 1282 | 2595 | a | 0 | + | | chr1 | 459010 | 466695 | a | 0 | + | | chr1 | 65794 | 67331 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6735724 | 6743336 | a | 0 | + | | chr1 | 6735724 | 6740604 | a | 0 | + | | chr1 | 4375529 | 4379633 | a | 0 | + | | chr19 | 6735724 | 6741209 | a | 0 | + | | chrX | 6735724 | 6745679 | a | 0 | + | | chrY | 6735724 | 6743860 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_g5iygzp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4375529 4379633 a 0 + 1 1 chr1 6735724 6740604 a 0 + 2 2 chr1 6735724 6743336 a 0 + 2 3 chr19 6735724 6741209 a 0 + 3 4 chrX 6735724 6745679 a 0 + 4 5 chrY 6735724 6743860 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6735724 | 6743336 | a | 0 | + | | chr1 | 6735724 | 6740604 | a | 0 | + | | chr1 | 4375529 | 4379633 | a | 0 | + | | chr19 | 6735724 | 6741209 | a | 0 | + | | chrX | 6735724 | 6745679 | a | 0 | + | | chrY | 6735724 | 6743860 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6735724 | 6743336 | a | 0 | + | | chr1 | 6735724 | 6740604 | a | 0 | + | | chr1 | 4375529 | 4379633 | a | 0 | + | | chr19 | 6735724 | 6741209 | a | 0 | + | | chrX | 6735724 | 6745679 | a | 0 | + | | chrX | 6735724 | 6743860 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpg2ejofxl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4375529 4379633 a 0 + 1 1 chr1 6735724 6740604 a 0 + 2 2 chr1 6735724 6743336 a 0 + 2 3 chr19 6735724 6741209 a 0 + 3 4 chrX 6735724 6745679 a 0 + 4 5 chrX 6735724 6743860 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6735724 | 6743336 | a | 0 | + | | chr1 | 6735724 | 6740604 | a | 0 | + | | chr1 | 4375529 | 4379633 | a | 0 | + | | chr19 | 6735724 | 6741209 | a | 0 | + | | chrX | 6735724 | 6745679 | a | 0 | + | | chrX | 6735724 | 6743860 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpitugb3n6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpddtjniyf/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpbs0op1m0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpay1gii8d/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpwleslc3v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxeu864u7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqbfrkp5c/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp783exdrx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp8hapst12/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp6mkzeea8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpltbb62xr/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxpc0_ikt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9630091 | 9639372 | a | 0 | - | | chrM | 1 | 1702 | a | 0 | - | | chrM | 1126619 | 1136451 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpekxway_3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9630091 9639372 a 0 - 1 1 chrM 1 1702 a 0 - 2 2 chrM 1126619 1136451 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9630091 | 9639372 | a | 0 | - | | chrM | 1 | 1702 | a | 0 | - | | chrM | 1126619 | 1136451 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7389025 | 7396474 | a | 0 | + | | chr1 | 1135584 | 1138939 | a | 0 | + | | chr1 | 2389644 | 2392334 | a | 0 | + | | chr1 | 3124143 | 3124940 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 161343 | 171342 | a | 0 | + | | chr21 | 9554751 | 9554818 | a | 0 | - | | chrM | 1435151 | 1443578 | a | 0 | + | | chrX | 904886 | 909543 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5sc2xtos/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1135584 1138939 a 0 + 1 1 chr1 2389644 2392334 a 0 + 2 2 chr1 7389025 7396474 a 0 + 3 3 chr1 3124143 3124940 a 0 - 4 4 chr12 161343 171342 a 0 + 5 5 chr21 9554751 9554818 a 0 - 6 6 chr5 9308477 9309755 a 0 + 7 7 chrM 1435151 1443578 a 0 + 8 8 chrX 904886 909543 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7389025 | 7396474 | a | 0 | + | | chr1 | 1135584 | 1138939 | a | 0 | + | | chr1 | 2389644 | 2392334 | a | 0 | + | | chr1 | 3124143 | 3124940 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 161343 | 171342 | a | 0 | + | | chr21 | 9554751 | 9554818 | a | 0 | - | | chrM | 1435151 | 1443578 | a | 0 | + | | chrX | 904886 | 909543 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3138052 | 3143588 | a | 0 | + | | chr1 | 5001870 | 5001872 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp0yufwrkp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3138052 3143588 a 0 + 1 1 chr1 5001870 5001872 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3138052 | 3143588 | a | 0 | + | | chr1 | 5001870 | 5001872 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 766193 | 770711 | a | 0 | + | | chr1 | 5975526 | 5979655 | a | 0 | + | | chr1 | 7333760 | 7336965 | a | 0 | - | | chr17 | 4568650 | 4572721 | a | 0 | + | | chrY | 8451161 | 8451643 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpc0gwjtwx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 766193 770711 a 0 + 1 1 chr1 5975526 5979655 a 0 + 2 2 chr1 7333760 7336965 a 0 - 3 3 chr17 4568650 4572721 a 0 + 4 4 chrY 8451161 8451643 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 766193 | 770711 | a | 0 | + | | chr1 | 5975526 | 5979655 | a | 0 | + | | chr1 | 7333760 | 7336965 | a | 0 | - | | chr17 | 4568650 | 4572721 | a | 0 | + | | chrY | 8451161 | 8451643 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8286622 | 8289814 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpa_4j5v_u/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8286622 8289814 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8286622 | 8289814 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 5328562 | 5335015 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp95wp_pp5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr6 5328562 5335015 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 5328562 | 5335015 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 5774566 | 5780163 | a | 0 | + | | chr15 | 5430042 | 5432773 | a | 0 | + | | chr22 | 8479435 | 8485869 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpikfi8yrw/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr11 5774566 5780163 a 0 + 1 1 chr15 5430042 5432773 a 0 + 2 2 chr22 8479435 8485869 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 5774566 | 5780163 | a | 0 | + | | chr15 | 5430042 | 5432773 | a | 0 | + | | chr22 | 8479435 | 8485869 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4586784 | 4586785 | a | 0 | + | | chr1 | 1 | 7668 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxarue7ne/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 7668 a 0 + 1 1 chr1 4586784 4586785 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4586784 | 4586785 | a | 0 | + | | chr1 | 1 | 7668 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2817716 | 2826710 | a | 0 | + | | chr1 | 2817716 | 2825853 | a | 0 | + | | chr7 | 2817716 | 2826710 | a | 0 | + | | chr17 | 2817716 | 2826710 | a | 0 | + | | chr19 | 2817716 | 2826710 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpvry29c9g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2817716 2825853 a 0 + 1 1 chr1 2817716 2826710 a 0 + 1 2 chr17 2817716 2826710 a 0 + 2 3 chr19 2817716 2826710 a 0 + 3 4 chr7 2817716 2826710 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2817716 | 2826710 | a | 0 | + | | chr1 | 2817716 | 2825853 | a | 0 | + | | chr7 | 2817716 | 2826710 | a | 0 | + | | chr17 | 2817716 | 2826710 | a | 0 | + | | chr19 | 2817716 | 2826710 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9515859 | 9520073 | a | 0 | + | | chr1 | 2552606 | 2559206 | a | 0 | + | | chr1 | 7540693 | 7541210 | a | 0 | + | | chr1 | 1816045 | 1826044 | a | 0 | - | | chr1 | 7530755 | 7540755 | a | 0 | - | | chr1 | 4249912 | 4256453 | a | 0 | - | | chr14 | 2 | 6073 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_kkcsq_v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2552606 2559206 a 0 + 1 1 chr1 7540693 7541210 a 0 + 2 2 chr1 9515859 9520073 a 0 + 3 3 chr1 1816045 1826044 a 0 - 4 4 chr1 4249912 4256453 a 0 - 5 5 chr1 7530755 7540755 a 0 - 6 6 chr14 2 6073 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9515859 | 9520073 | a | 0 | + | | chr1 | 2552606 | 2559206 | a | 0 | + | | chr1 | 7540693 | 7541210 | a | 0 | + | | chr1 | 1816045 | 1826044 | a | 0 | - | | chr1 | 7530755 | 7540755 | a | 0 | - | | chr1 | 4249912 | 4256453 | a | 0 | - | | chr14 | 2 | 6073 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6790573 | 6794365 | a | 0 | + | | chr8 | 1694692 | 1699985 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpb99kwp8o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6790573 6794365 a 0 + 1 1 chr8 1694692 1699985 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6790573 | 6794365 | a | 0 | + | | chr8 | 1694692 | 1699985 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 663151 | 664192 | a | 0 | + | | chr1 | 1975135 | 1977965 | a | 0 | + | | chr1 | 6100087 | 6101732 | a | 0 | - | | chr4 | 4387355 | 4388245 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpiadtb4i2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 663151 664192 a 0 + 1 1 chr1 1975135 1977965 a 0 + 2 2 chr1 6100087 6101732 a 0 - 3 3 chr4 4387355 4388245 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 663151 | 664192 | a | 0 | + | | chr1 | 1975135 | 1977965 | a | 0 | + | | chr1 | 6100087 | 6101732 | a | 0 | - | | chr4 | 4387355 | 4388245 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9297258 | 9307231 | a | 0 | + | | chr1 | 228087 | 228919 | a | 0 | + | | chr1 | 1440782 | 1448952 | a | 0 | + | | chr1 | 6305693 | 6308872 | a | 0 | + | | chr2 | 1440782 | 1441389 | a | 0 | + | | chr6 | 4865772 | 4875772 | a | 0 | - | | chr7 | 1440782 | 1447027 | a | 0 | - | | chrX | 4517321 | 4525491 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpy04rnsp_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 228087 228919 a 0 + 1 1 chr1 1440782 1448952 a 0 + 2 2 chr1 6305693 6308872 a 0 + 3 3 chr1 9297258 9307231 a 0 + 4 4 chr2 1440782 1441389 a 0 + 5 5 chr6 4865772 4875772 a 0 - 6 6 chr7 1440782 1447027 a 0 - 7 7 chrX 4517321 4525491 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9297258 | 9307231 | a | 0 | + | | chr1 | 228087 | 228919 | a | 0 | + | | chr1 | 1440782 | 1448952 | a | 0 | + | | chr1 | 6305693 | 6308872 | a | 0 | + | | chr2 | 1440782 | 1441389 | a | 0 | + | | chr6 | 4865772 | 4875772 | a | 0 | - | | chr7 | 1440782 | 1447027 | a | 0 | - | | chrX | 4517321 | 4525491 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10009348 | a | 0 | + | | chr1 | 5511748 | 5512393 | a | 0 | - | | chr16 | 3871268 | 3875995 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpegp8n787/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 10000000 10009348 a 0 + 1 1 chr1 5511748 5512393 a 0 - 2 2 chr16 3871268 3875995 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10009348 | a | 0 | + | | chr1 | 5511748 | 5512393 | a | 0 | - | | chr16 | 3871268 | 3875995 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8619245 | 8626572 | a | 0 | + | | chr1 | 2427682 | 2430550 | a | 0 | - | | chr8 | 2106606 | 2111210 | a | 0 | - | | chr9 | 3757595 | 3767263 | a | 0 | + | | chr15 | 1122278 | 1129817 | a | 0 | - | | chr21 | 3878346 | 3884134 | a | 0 | - | | chrY | 2965984 | 2973420 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxota5xi7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8619245 8626572 a 0 + 1 1 chr1 2427682 2430550 a 0 - 2 2 chr15 1122278 1129817 a 0 - 3 3 chr21 3878346 3884134 a 0 - 4 4 chr8 2106606 2111210 a 0 - 5 5 chr9 3757595 3767263 a 0 + 6 6 chrY 2965984 2973420 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8619245 | 8626572 | a | 0 | + | | chr1 | 2427682 | 2430550 | a | 0 | - | | chr8 | 2106606 | 2111210 | a | 0 | - | | chr9 | 3757595 | 3767263 | a | 0 | + | | chr15 | 1122278 | 1129817 | a | 0 | - | | chr21 | 3878346 | 3884134 | a | 0 | - | | chrY | 2965984 | 2973420 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8171670 | 8180426 | a | 0 | + | | chr1 | 4888491 | 4895748 | a | 0 | + | | chr1 | 9471482 | 9477677 | a | 0 | - | | chr13 | 4421672 | 4426988 | a | 0 | - | | chr16 | 4962830 | 4970525 | a | 0 | + | | chr16 | 2399541 | 2405056 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpa58mlebi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4888491 4895748 a 0 + 1 1 chr1 8171670 8180426 a 0 + 2 2 chr1 9471482 9477677 a 0 - 3 3 chr13 4421672 4426988 a 0 - 4 4 chr16 4962830 4970525 a 0 + 5 5 chr16 2399541 2405056 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8171670 | 8180426 | a | 0 | + | | chr1 | 4888491 | 4895748 | a | 0 | + | | chr1 | 9471482 | 9477677 | a | 0 | - | | chr13 | 4421672 | 4426988 | a | 0 | - | | chr16 | 4962830 | 4970525 | a | 0 | + | | chr16 | 2399541 | 2405056 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8047051 | 8056640 | a | 0 | - | | chr1 | 4523040 | 4529854 | a | 0 | - | | chr1 | 5600150 | 5603583 | a | 0 | - | | chr1 | 3256467 | 3259908 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 5687906 | 5688449 | a | 0 | - | | chr14 | 5687906 | 5693846 | a | 0 | - | | chrY | 7301810 | 7307996 | a | 0 | - | | chrY | 5687906 | 5690649 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpgdejwpx6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3256467 3259908 a 0 - 1 1 chr1 4523040 4529854 a 0 - 2 2 chr1 5600150 5603583 a 0 - 3 3 chr1 7489519 7490702 a 0 - 4 4 chr1 8047051 8056640 a 0 - 5 5 chr1 8985055 8994543 a 0 - 6 6 chr14 5687906 5693846 a 0 - 7 7 chr3 9979268 9981304 a 0 + 8 8 chr9 5687906 5688449 a 0 - 9 9 chrY 5687906 5690649 a 0 - 10 10 chrY 7301810 7307996 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8047051 | 8056640 | a | 0 | - | | chr1 | 4523040 | 4529854 | a | 0 | - | | chr1 | 5600150 | 5603583 | a | 0 | - | | chr1 | 3256467 | 3259908 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 5687906 | 5688449 | a | 0 | - | | chr14 | 5687906 | 5693846 | a | 0 | - | | chrY | 7301810 | 7307996 | a | 0 | - | | chrY | 5687906 | 5690649 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5681917 | 5683575 | a | 0 | - | | chr1 | 8911533 | 8920884 | a | 0 | - | | chr2 | 5681917 | 5691488 | a | 0 | + | | chr2 | 1858089 | 1865055 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 8132790 | 8142079 | a | 0 | + | | chr5 | 1606329 | 1615383 | a | 0 | + | | chr5 | 1374749 | 1381937 | a | 0 | - | | chr5 | 1470048 | 1476500 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdtsomros/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5681917 5683575 a 0 - 1 1 chr1 8911533 8920884 a 0 - 2 2 chr2 1858089 1865055 a 0 + 3 3 chr2 5681917 5691488 a 0 + 4 4 chr5 2 3 a 0 + 5 5 chr5 1606329 1615383 a 0 + 6 6 chr5 8132790 8142079 a 0 + 7 7 chr5 8603496 8611547 a 0 + 8 8 chr5 9999999 10008564 a 0 + 9 9 chr5 1374749 1381937 a 0 - 10 10 chr5 1470048 1476500 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5681917 | 5683575 | a | 0 | - | | chr1 | 8911533 | 8920884 | a | 0 | - | | chr2 | 5681917 | 5691488 | a | 0 | + | | chr2 | 1858089 | 1865055 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 8132790 | 8142079 | a | 0 | + | | chr5 | 1606329 | 1615383 | a | 0 | + | | chr5 | 1374749 | 1381937 | a | 0 | - | | chr5 | 1470048 | 1476500 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8167564 | 8176588 | a | 0 | + | | chr1 | 1133305 | 1141060 | a | 0 | - | | chr18 | 8317453 | 8318000 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpt59zuhft/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8167564 8176588 a 0 + 1 1 chr1 1133305 1141060 a 0 - 2 2 chr18 8317453 8318000 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8167564 | 8176588 | a | 0 | + | | chr1 | 1133305 | 1141060 | a | 0 | - | | chr18 | 8317453 | 8318000 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 2112920 | 2113656 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp562t_bxb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 2112920 2113656 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 2112920 | 2113656 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 5003813 | 5011567 | a | 0 | + | | chr5 | 180482 | 188367 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpbzghu7w0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr3 5003813 5011567 a 0 + 1 1 chr5 180482 188367 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 5003813 | 5011567 | a | 0 | + | | chr5 | 180482 | 188367 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2678703 | 2678884 | a | 0 | - | | chr1 | 6464209 | 6464211 | a | 0 | - | | chr1 | 9219968 | 9219970 | a | 0 | - | | chr1 | 5102279 | 5102281 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 1575504 | 1575506 | a | 0 | - | | chrX | 2364255 | 2364257 | a | 0 | + | | chrY | 7212259 | 7218081 | a | 0 | + | | chrY | 5988461 | 5988463 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpb1revkoy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2678703 2678884 a 0 - 1 1 chr1 5102279 5102281 a 0 - 2 2 chr1 6464209 6464211 a 0 - 3 3 chr1 9219968 9219970 a 0 - 4 4 chr3 4570031 4570033 a 0 - 5 5 chr5 89179 89181 a 0 + 6 6 chr6 272152 272154 a 0 + 7 7 chr7 1575504 1575506 a 0 - 8 8 chrX 2364255 2364257 a 0 + 9 9 chrY 7212259 7218081 a 0 + 10 10 chrY 5988461 5988463 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2678703 | 2678884 | a | 0 | - | | chr1 | 6464209 | 6464211 | a | 0 | - | | chr1 | 9219968 | 9219970 | a | 0 | - | | chr1 | 5102279 | 5102281 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 1575504 | 1575506 | a | 0 | - | | chrX | 2364255 | 2364257 | a | 0 | + | | chrY | 7212259 | 7218081 | a | 0 | + | | chrY | 5988461 | 5988463 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 5349260 | 5354911 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzjyaw8n0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr3 5349260 5354911 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 5349260 | 5354911 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 816950 | 826755 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpndk6sse4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 816950 826755 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 816950 | 826755 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5425249 | 5429578 | a | 0 | + | | chr1 | 6166617 | 6174437 | a | 0 | + | | chr1 | 2214054 | 2219165 | a | 0 | - | | chr1 | 5354252 | 5364252 | a | 0 | - | | chr5 | 9546302 | 9546949 | a | 0 | + | | chr6 | 4507308 | 4512485 | a | 0 | - | | chr10 | 4276651 | 4281461 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp26ms6bog/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5425249 5429578 a 0 + 1 1 chr1 6166617 6174437 a 0 + 2 2 chr1 2214054 2219165 a 0 - 3 3 chr1 5354252 5364252 a 0 - 4 4 chr10 4276651 4281461 a 0 - 5 5 chr5 9546302 9546949 a 0 + 6 6 chr6 4507308 4512485 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5425249 | 5429578 | a | 0 | + | | chr1 | 6166617 | 6174437 | a | 0 | + | | chr1 | 2214054 | 2219165 | a | 0 | - | | chr1 | 5354252 | 5364252 | a | 0 | - | | chr5 | 9546302 | 9546949 | a | 0 | + | | chr6 | 4507308 | 4512485 | a | 0 | - | | chr10 | 4276651 | 4281461 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6867539 | 6870477 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpusiu08ky/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6867539 6870477 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6867539 | 6870477 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5082002 | 5087950 | a | 0 | + | | chr1 | 4242284 | 4251875 | a | 0 | + | | chr1 | 282005 | 287953 | a | 0 | + | | chr1 | 8553630 | 8559578 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr11 | 5082002 | 5085590 | a | 0 | + | | chr11 | 1542001 | 1547949 | a | 0 | - | | chr15 | 3654141 | 3660089 | a | 0 | + | | chr18 | 4661080 | 4667028 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp995ludpe/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 282005 287953 a 0 + 1 1 chr1 4242284 4251875 a 0 + 2 2 chr1 5082002 5087950 a 0 + 3 3 chr1 8553630 8559578 a 0 + 4 4 chr1 5082002 5084505 a 0 - 5 5 chr11 5082002 5085590 a 0 + 6 6 chr11 1542001 1547949 a 0 - 7 7 chr15 3654141 3660089 a 0 + 8 8 chr18 4661080 4667028 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5082002 | 5087950 | a | 0 | + | | chr1 | 4242284 | 4251875 | a | 0 | + | | chr1 | 282005 | 287953 | a | 0 | + | | chr1 | 8553630 | 8559578 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr11 | 5082002 | 5085590 | a | 0 | + | | chr11 | 1542001 | 1547949 | a | 0 | - | | chr15 | 3654141 | 3660089 | a | 0 | + | | chr18 | 4661080 | 4667028 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3797809 | 3805851 | a | 0 | + | | chr1 | 7343199 | 7352019 | a | 0 | - | | chr14 | 9915111 | 9924626 | a | 0 | + | | chr14 | 163247 | 168896 | a | 0 | + | | chr19 | 7509089 | 7513218 | a | 0 | + | | chr20 | 5874960 | 5880291 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpl8slvddj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3797809 3805851 a 0 + 1 1 chr1 7343199 7352019 a 0 - 2 2 chr14 163247 168896 a 0 + 3 3 chr14 9915111 9924626 a 0 + 4 4 chr19 7509089 7513218 a 0 + 5 5 chr20 5874960 5880291 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3797809 | 3805851 | a | 0 | + | | chr1 | 7343199 | 7352019 | a | 0 | - | | chr14 | 9915111 | 9924626 | a | 0 | + | | chr14 | 163247 | 168896 | a | 0 | + | | chr19 | 7509089 | 7513218 | a | 0 | + | | chr20 | 5874960 | 5880291 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 449479 | 459113 | a | 0 | + | | chr1 | 8797692 | 8799452 | a | 0 | - | | chr1 | 6776463 | 6780475 | a | 0 | - | | chr2 | 1486491 | 1493596 | a | 0 | - | | chrX | 4212437 | 4220820 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_rvg476e/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 449479 459113 a 0 + 1 1 chr1 6776463 6780475 a 0 - 2 2 chr1 8797692 8799452 a 0 - 3 3 chr2 1486491 1493596 a 0 - 4 4 chrX 4212437 4220820 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 449479 | 459113 | a | 0 | + | | chr1 | 8797692 | 8799452 | a | 0 | - | | chr1 | 6776463 | 6780475 | a | 0 | - | | chr2 | 1486491 | 1493596 | a | 0 | - | | chrX | 4212437 | 4220820 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7644387 | 7649925 | a | 0 | + | | chr1 | 6238101 | 6245862 | a | 0 | + | | chr1 | 5236765 | 5238081 | a | 0 | - | | chr9 | 4626989 | 4630159 | a | 0 | - | | chr11 | 6862087 | 6868871 | a | 0 | + | | chr12 | 2334971 | 2338141 | a | 0 | - | | chr22 | 2273503 | 2282816 | a | 0 | + | | chrM | 1597718 | 1601933 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpj9lak97f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6238101 6245862 a 0 + 1 1 chr1 7644387 7649925 a 0 + 2 2 chr1 5236765 5238081 a 0 - 3 3 chr11 6862087 6868871 a 0 + 4 4 chr12 2334971 2338141 a 0 - 5 5 chr22 2273503 2282816 a 0 + 6 6 chr9 4626989 4630159 a 0 - 7 7 chrM 1597718 1601933 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7644387 | 7649925 | a | 0 | + | | chr1 | 6238101 | 6245862 | a | 0 | + | | chr1 | 5236765 | 5238081 | a | 0 | - | | chr9 | 4626989 | 4630159 | a | 0 | - | | chr11 | 6862087 | 6868871 | a | 0 | + | | chr12 | 2334971 | 2338141 | a | 0 | - | | chr22 | 2273503 | 2282816 | a | 0 | + | | chrM | 1597718 | 1601933 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1051699 | 1059526 | a | 0 | - | | chr1 | 8632860 | 8635155 | a | 0 | - | | chr1 | 1645515 | 1655061 | a | 0 | - | | chr1 | 9824891 | 9828306 | a | 0 | - | | chr10 | 3097053 | 3105131 | a | 0 | + | | chr12 | 7502166 | 7505624 | a | 0 | + | | chr12 | 7276372 | 7285245 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9l9th5zh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1051699 1059526 a 0 - 1 1 chr1 1645515 1655061 a 0 - 2 2 chr1 8632860 8635155 a 0 - 3 3 chr1 9824891 9828306 a 0 - 4 4 chr10 3097053 3105131 a 0 + 5 5 chr12 7502166 7505624 a 0 + 6 6 chr12 7276372 7285245 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1051699 | 1059526 | a | 0 | - | | chr1 | 8632860 | 8635155 | a | 0 | - | | chr1 | 1645515 | 1655061 | a | 0 | - | | chr1 | 9824891 | 9828306 | a | 0 | - | | chr10 | 3097053 | 3105131 | a | 0 | + | | chr12 | 7502166 | 7505624 | a | 0 | + | | chr12 | 7276372 | 7285245 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5852053 | 5855982 | a | 0 | + | | chr1 | 7852692 | 7856621 | a | 0 | + | | chr1 | 5782918 | 5786847 | a | 0 | - | | chr1 | 5355877 | 5359806 | a | 0 | - | | chr5 | 7580197 | 7584126 | a | 0 | + | | chr15 | 8071187 | 8075116 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmplrk1x3q6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5852053 5855982 a 0 + 1 1 chr1 7852692 7856621 a 0 + 2 2 chr1 5355877 5359806 a 0 - 3 3 chr1 5782918 5786847 a 0 - 4 4 chr15 8071187 8075116 a 0 - 5 5 chr5 7580197 7584126 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5852053 | 5855982 | a | 0 | + | | chr1 | 7852692 | 7856621 | a | 0 | + | | chr1 | 5782918 | 5786847 | a | 0 | - | | chr1 | 5355877 | 5359806 | a | 0 | - | | chr5 | 7580197 | 7584126 | a | 0 | + | | chr15 | 8071187 | 8075116 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 6663619 | 6668038 | a | 0 | + | | chrY | 4385908 | 4390921 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpe0823pv7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr2 6663619 6668038 a 0 + 1 1 chrY 4385908 4390921 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 6663619 | 6668038 | a | 0 | + | | chrY | 4385908 | 4390921 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 9863824 | 9865448 | a | 0 | - | | chr21 | 8013538 | 8017222 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpc_qby6et/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr15 9863824 9865448 a 0 - 1 1 chr21 8013538 8017222 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 9863824 | 9865448 | a | 0 | - | | chr21 | 8013538 | 8017222 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6338936 | 6343470 | a | 0 | - | | chr2 | 1372523 | 1379736 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzyha_7ee/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6338936 6343470 a 0 - 1 1 chr2 1372523 1379736 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6338936 | 6343470 | a | 0 | - | | chr2 | 1372523 | 1379736 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3781414 | 3791381 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp93md2uh7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3781414 3791381 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3781414 | 3791381 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4229113 | 4231583 | a | 0 | - | | chr12 | 4229113 | 4232718 | a | 0 | - | | chr21 | 4229113 | 4235478 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmptrd97bpt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4229113 4231583 a 0 - 1 1 chr12 4229113 4232718 a 0 - 2 2 chr21 4229113 4235478 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4229113 | 4231583 | a | 0 | - | | chr12 | 4229113 | 4232718 | a | 0 | - | | chr21 | 4229113 | 4235478 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3901510 | 3901602 | a | 0 | + | | chr1 | 4972786 | 4976378 | a | 0 | - | | chr2 | 2221635 | 2225357 | a | 0 | - | | chr12 | 7407541 | 7413347 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpw1c1y1c5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3901510 3901602 a 0 + 1 1 chr1 4972786 4976378 a 0 - 2 2 chr12 7407541 7413347 a 0 + 3 3 chr2 2221635 2225357 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3901510 | 3901602 | a | 0 | + | | chr1 | 4972786 | 4976378 | a | 0 | - | | chr2 | 2221635 | 2225357 | a | 0 | - | | chr12 | 7407541 | 7413347 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 3320447 | 3324511 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp3duefobi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr3 3320447 3324511 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 3320447 | 3324511 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 9598385 | 9605186 | a | 0 | - | | chr13 | 5043191 | 5045446 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpptqexa8a/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr13 5043191 5045446 a 0 - 1 1 chr5 9598385 9605186 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 9598385 | 9605186 | a | 0 | - | | chr13 | 5043191 | 5045446 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6537340 | 6538608 | a | 0 | + | | chr1 | 9418194 | 9426770 | a | 0 | + | | chr1 | 4916725 | 4926297 | a | 0 | - | | chr1 | 395627 | 402969 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 2608481 | 2608746 | a | 0 | - | | chr8 | 5988329 | 5996249 | a | 0 | + | | chr12 | 7722804 | 7729050 | a | 0 | + | | chr12 | 5902915 | 5904130 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmphz46m2bl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6537340 6538608 a 0 + 1 1 chr1 9418194 9426770 a 0 + 2 2 chr1 395627 402969 a 0 - 3 3 chr1 2608481 2611645 a 0 - 4 4 chr1 3476030 3479638 a 0 - 5 5 chr1 4916725 4926297 a 0 - 6 6 chr1 5395482 5395483 a 0 - 7 7 chr12 7722804 7729050 a 0 + 8 8 chr12 5902915 5904130 a 0 - 9 9 chr7 2608481 2608746 a 0 - 10 10 chr8 5988329 5996249 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6537340 | 6538608 | a | 0 | + | | chr1 | 9418194 | 9426770 | a | 0 | + | | chr1 | 4916725 | 4926297 | a | 0 | - | | chr1 | 395627 | 402969 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 2608481 | 2608746 | a | 0 | - | | chr8 | 5988329 | 5996249 | a | 0 | + | | chr12 | 7722804 | 7729050 | a | 0 | + | | chr12 | 5902915 | 5904130 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3725434 | 3729518 | a | 0 | + | | chr1 | 5960913 | 5963864 | a | 0 | - | | chr1 | 356380 | 358390 | a | 0 | - | | chr7 | 3408117 | 3411321 | a | 0 | - | | chr15 | 9655731 | 9664976 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp66uyde5u/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3725434 3729518 a 0 + 1 1 chr1 356380 358390 a 0 - 2 2 chr1 5960913 5963864 a 0 - 3 3 chr15 9655731 9664976 a 0 + 4 4 chr7 3408117 3411321 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3725434 | 3729518 | a | 0 | + | | chr1 | 5960913 | 5963864 | a | 0 | - | | chr1 | 356380 | 358390 | a | 0 | - | | chr7 | 3408117 | 3411321 | a | 0 | - | | chr15 | 9655731 | 9664976 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6715710 | 6723426 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpeoejmpi6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6715710 6723426 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6715710 | 6723426 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2158200 | 2165746 | a | 0 | + | | chr1 | 6943392 | 6944363 | a | 0 | + | | chr1 | 8693291 | 8694815 | a | 0 | - | | chr5 | 235329 | 236300 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 5878390 | 5879361 | a | 0 | + | | chr18 | 2569549 | 2578381 | a | 0 | + | | chr21 | 6943392 | 6946060 | a | 0 | + | | chrM | 7123877 | 7131420 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7kjstozp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2158200 2165746 a 0 + 1 1 chr1 6943392 6944363 a 0 + 2 2 chr1 8693291 8694815 a 0 - 3 3 chr13 62942 62943 a 0 - 4 4 chr16 5878390 5879361 a 0 + 5 5 chr18 2569549 2578381 a 0 + 6 6 chr21 6943392 6946060 a 0 + 7 7 chr5 235329 236300 a 0 + 8 8 chrM 7123877 7131420 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2158200 | 2165746 | a | 0 | + | | chr1 | 6943392 | 6944363 | a | 0 | + | | chr1 | 8693291 | 8694815 | a | 0 | - | | chr5 | 235329 | 236300 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 5878390 | 5879361 | a | 0 | + | | chr18 | 2569549 | 2578381 | a | 0 | + | | chr21 | 6943392 | 6946060 | a | 0 | + | | chrM | 7123877 | 7131420 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1308590 | 1316989 | a | 0 | - | | chr1 | 7493736 | 7494091 | a | 0 | - | | chr1 | 1308590 | 1315909 | a | 0 | - | | chr1 | 1308590 | 1316265 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1308590 | 1316265 | a | 0 | - | | chr1 | 1977246 | 1986303 | a | 0 | - | | chr1 | 9999999 | 10005469 | a | 0 | - | | chr1 | 1055174 | 1058907 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_j32ac0r/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1055174 1058907 a 0 - 1 1 chr1 1308590 1315909 a 0 - 2 2 chr1 1308590 1316265 a 0 - 2 3 chr1 1308590 1316989 a 0 - 2 4 chr1 1977246 1986303 a 0 - 3 5 chr1 7493736 7494091 a 0 - 4 6 chr1 9999999 10005469 a 0 - 5 7 chr10 9431827 9438366 a 0 - 6 8 chr13 7185497 7192548 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1308590 | 1316989 | a | 0 | - | | chr1 | 7493736 | 7494091 | a | 0 | - | | chr1 | 1308590 | 1315909 | a | 0 | - | | chr1 | 1308590 | 1316265 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1308590 | 1316265 | a | 0 | - | | chr1 | 1977246 | 1986303 | a | 0 | - | | chr1 | 9999999 | 10005469 | a | 0 | - | | chr1 | 1055174 | 1058907 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6063714 | 6067812 | a | 0 | + | | chr1 | 3929070 | 3933374 | a | 0 | - | | chr1 | 3343345 | 3351172 | a | 0 | - | | chr11 | 8622949 | 8623094 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmppmbc3ri4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6063714 6067812 a 0 + 1 1 chr1 3343345 3351172 a 0 - 2 2 chr1 3929070 3933374 a 0 - 3 3 chr11 8622949 8623094 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6063714 | 6067812 | a | 0 | + | | chr1 | 3929070 | 3933374 | a | 0 | - | | chr1 | 3343345 | 3351172 | a | 0 | - | | chr11 | 8622949 | 8623094 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr20 | 8048197 | 8056645 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp8ew4dz0k/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr20 8048197 8056645 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr20 | 8048197 | 8056645 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5736347 | 5744138 | a | 0 | - | | chr1 | 3194232 | 3199015 | a | 0 | - | | chr1 | 6873314 | 6878097 | a | 0 | - | | chr21 | 3184410 | 3189193 | a | 0 | - | | chr22 | 5473682 | 5478465 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp85pmxdj1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3194232 3199015 a 0 - 1 1 chr1 5736347 5744138 a 0 - 2 2 chr1 6873314 6878097 a 0 - 3 3 chr21 3184410 3189193 a 0 - 4 4 chr22 5473682 5478465 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5736347 | 5744138 | a | 0 | - | | chr1 | 3194232 | 3199015 | a | 0 | - | | chr1 | 6873314 | 6878097 | a | 0 | - | | chr21 | 3184410 | 3189193 | a | 0 | - | | chr22 | 5473682 | 5478465 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2660549 | 2660690 | a | 0 | + | | chr1 | 6585135 | 6585276 | a | 0 | - | | chr1 | 3973127 | 3973268 | a | 0 | - | | chr1 | 4460070 | 4460211 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 59422 | 59563 | a | 0 | - | | chr12 | 7390021 | 7390321 | a | 0 | + | | chr21 | 3619290 | 3619431 | a | 0 | - | | chrM | 2073955 | 2075368 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpn1ehjspx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2660549 2660690 a 0 + 1 1 chr1 3361478 3371477 a 0 - 2 2 chr1 3973127 3973268 a 0 - 3 3 chr1 4460070 4460211 a 0 - 4 4 chr1 5595547 5595688 a 0 - 5 5 chr1 6585135 6585276 a 0 - 6 6 chr1 7009344 7009485 a 0 - 7 7 chr12 7390021 7390321 a 0 + 8 8 chr21 3619290 3619431 a 0 - 9 9 chr5 59422 59563 a 0 - 10 10 chrM 2073955 2075368 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2660549 | 2660690 | a | 0 | + | | chr1 | 6585135 | 6585276 | a | 0 | - | | chr1 | 3973127 | 3973268 | a | 0 | - | | chr1 | 4460070 | 4460211 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 59422 | 59563 | a | 0 | - | | chr12 | 7390021 | 7390321 | a | 0 | + | | chr21 | 3619290 | 3619431 | a | 0 | - | | chrM | 2073955 | 2075368 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9007630 | 9014550 | a | 0 | + | | chr1 | 6221563 | 6231256 | a | 0 | + | | chr1 | 9323594 | 9324575 | a | 0 | - | | chr1 | 3130120 | 3133638 | a | 0 | - | | chr1 | 1668863 | 1671290 | a | 0 | - | | chr1 | 1988244 | 1988245 | a | 0 | - | | chr14 | 1587707 | 1590527 | a | 0 | - | | chr21 | 3285665 | 3295035 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdkxwvxga/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6221563 6231256 a 0 + 1 1 chr1 9007630 9014550 a 0 + 2 2 chr1 1668863 1671290 a 0 - 3 3 chr1 1988244 1988245 a 0 - 4 4 chr1 3130120 3133638 a 0 - 5 5 chr1 9323594 9324575 a 0 - 6 6 chr14 1587707 1590527 a 0 - 7 7 chr21 3285665 3295035 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9007630 | 9014550 | a | 0 | + | | chr1 | 6221563 | 6231256 | a | 0 | + | | chr1 | 9323594 | 9324575 | a | 0 | - | | chr1 | 3130120 | 3133638 | a | 0 | - | | chr1 | 1668863 | 1671290 | a | 0 | - | | chr1 | 1988244 | 1988245 | a | 0 | - | | chr14 | 1587707 | 1590527 | a | 0 | - | | chr21 | 3285665 | 3295035 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6591352 | 6597301 | a | 0 | + | | chr1 | 1120361 | 1129578 | a | 0 | + | | chr1 | 921276 | 928273 | a | 0 | + | | chr1 | 400522 | 400554 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 7882144 | 7883137 | a | 0 | + | | chr12 | 4817155 | 4818335 | a | 0 | - | | chr21 | 2503885 | 2508923 | a | 0 | - | | chrX | 2793244 | 2796060 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpyib_kq3j/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 921276 928273 a 0 + 1 1 chr1 1120361 1129578 a 0 + 2 2 chr1 6591352 6597301 a 0 + 3 3 chr1 400522 400554 a 0 - 4 4 chr11 7882144 7883137 a 0 + 5 5 chr12 4817155 4818335 a 0 - 6 6 chr2 9876759 9880005 a 0 + 7 7 chr21 2503885 2508923 a 0 - 8 8 chr7 5602210 5605542 a 0 - 9 9 chr8 6247967 6257967 a 0 - 10 10 chrX 2793244 2796060 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6591352 | 6597301 | a | 0 | + | | chr1 | 1120361 | 1129578 | a | 0 | + | | chr1 | 921276 | 928273 | a | 0 | + | | chr1 | 400522 | 400554 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 7882144 | 7883137 | a | 0 | + | | chr12 | 4817155 | 4818335 | a | 0 | - | | chr21 | 2503885 | 2508923 | a | 0 | - | | chrX | 2793244 | 2796060 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3448167 | 3456963 | a | 0 | - | | chr1 | 9547771 | 9555654 | a | 0 | - | | chr1 | 4648229 | 4654553 | a | 0 | - | | chr1 | 2311871 | 2317059 | a | 0 | - | | chr2 | 440826 | 448161 | a | 0 | + | | chr3 | 3583686 | 3588197 | a | 0 | + | | chr18 | 7517610 | 7523837 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpprxfqkz0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2311871 2317059 a 0 - 1 1 chr1 3448167 3456963 a 0 - 2 2 chr1 4648229 4654553 a 0 - 3 3 chr1 9547771 9555654 a 0 - 4 4 chr18 7517610 7523837 a 0 + 5 5 chr2 440826 448161 a 0 + 6 6 chr3 3583686 3588197 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3448167 | 3456963 | a | 0 | - | | chr1 | 9547771 | 9555654 | a | 0 | - | | chr1 | 4648229 | 4654553 | a | 0 | - | | chr1 | 2311871 | 2317059 | a | 0 | - | | chr2 | 440826 | 448161 | a | 0 | + | | chr3 | 3583686 | 3588197 | a | 0 | + | | chr18 | 7517610 | 7523837 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 4816251 | 4822831 | a | 0 | + | | chr19 | 3842732 | 3843632 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpjj00uieo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr11 4816251 4822831 a 0 + 1 1 chr19 3842732 3843632 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 4816251 | 4822831 | a | 0 | + | | chr19 | 3842732 | 3843632 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 5127983 | 5135429 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmprjvwkabh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chrY 5127983 5135429 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 5127983 | 5135429 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3539367 | 3547673 | a | 0 | + | | chr1 | 3648563 | 3651193 | a | 0 | + | | chr1 | 3525907 | 3535889 | a | 0 | + | | chr1 | 9617107 | 9625413 | a | 0 | - | | chr1 | 3889837 | 3898311 | a | 0 | - | | chr1 | 4273148 | 4281454 | a | 0 | - | | chr4 | 3889837 | 3899837 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp82s2aa2u/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3525907 3535889 a 0 + 1 1 chr1 3539367 3547673 a 0 + 2 2 chr1 3648563 3651193 a 0 + 3 3 chr1 3889837 3898311 a 0 - 4 4 chr1 4273148 4281454 a 0 - 5 5 chr1 9617107 9625413 a 0 - 6 6 chr4 3889837 3899837 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3539367 | 3547673 | a | 0 | + | | chr1 | 3648563 | 3651193 | a | 0 | + | | chr1 | 3525907 | 3535889 | a | 0 | + | | chr1 | 9617107 | 9625413 | a | 0 | - | | chr1 | 3889837 | 3898311 | a | 0 | - | | chr1 | 4273148 | 4281454 | a | 0 | - | | chr4 | 3889837 | 3899837 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 9464232 | 9469295 | a | 0 | + | | chr12 | 2971589 | 2974907 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpn0c57xi5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr12 2971589 2974907 a 0 - 1 1 chr8 9464232 9469295 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 9464232 | 9469295 | a | 0 | + | | chr12 | 2971589 | 2974907 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5789713 | 5797985 | a | 0 | - | | chr1 | 8877327 | 8877868 | a | 0 | - | | chr1 | 1637166 | 1642886 | a | 0 | - | | chr1 | 7357612 | 7364869 | a | 0 | - | | chr17 | 4908938 | 4914327 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp1z9q1l_k/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1637166 1642886 a 0 - 1 1 chr1 5789713 5797985 a 0 - 2 2 chr1 7357612 7364869 a 0 - 3 3 chr1 8877327 8877868 a 0 - 4 4 chr17 4908938 4914327 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5789713 | 5797985 | a | 0 | - | | chr1 | 8877327 | 8877868 | a | 0 | - | | chr1 | 1637166 | 1642886 | a | 0 | - | | chr1 | 7357612 | 7364869 | a | 0 | - | | chr17 | 4908938 | 4914327 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3364541 | 3367234 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzqfwq1eh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3364541 3367234 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3364541 | 3367234 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5315574 | 5318911 | a | 0 | + | | chr1 | 7829115 | 7836392 | a | 0 | + | | chr1 | 2505355 | 2511354 | a | 0 | + | | chr1 | 6214648 | 6217630 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1629231 | 1638533 | a | 0 | - | | chr1 | 2869147 | 2870498 | a | 0 | - | | chr1 | 4665399 | 4671547 | a | 0 | - | | chr1 | 7839605 | 7839606 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpkexyhor1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2505355 2511354 a 0 + 1 1 chr1 5315574 5318911 a 0 + 2 2 chr1 6214648 6217630 a 0 + 3 3 chr1 7829115 7836392 a 0 + 4 4 chr1 1629231 1638533 a 0 - 5 5 chr1 2869147 2870498 a 0 - 6 6 chr1 4665399 4671547 a 0 - 7 7 chr1 7839605 7839606 a 0 - 8 8 chr19 6550508 6554328 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5315574 | 5318911 | a | 0 | + | | chr1 | 7829115 | 7836392 | a | 0 | + | | chr1 | 2505355 | 2511354 | a | 0 | + | | chr1 | 6214648 | 6217630 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1629231 | 1638533 | a | 0 | - | | chr1 | 2869147 | 2870498 | a | 0 | - | | chr1 | 4665399 | 4671547 | a | 0 | - | | chr1 | 7839605 | 7839606 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6612348 | 6614881 | a | 0 | + | | chr1 | 51342 | 61311 | a | 0 | - | | chr2 | 51342 | 51544 | a | 0 | - | | chr2 | 7607576 | 7616894 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 9467564 | 9477523 | a | 0 | - | | chr15 | 3130547 | 3138411 | a | 0 | - | | chr19 | 4480036 | 4482016 | a | 0 | - | | chr22 | 9816457 | 9825238 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpg8c92i_m/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6612348 6614881 a 0 + 1 1 chr1 51342 61311 a 0 - 2 2 chr11 6311178 6320000 a 0 + 3 3 chr12 1180681 1180910 a 0 + 4 4 chr12 5787088 5793789 a 0 - 5 5 chr13 9467564 9477523 a 0 - 6 6 chr15 3130547 3138411 a 0 - 7 7 chr19 4480036 4482016 a 0 - 8 8 chr2 51342 51544 a 0 - 9 9 chr2 7607576 7616894 a 0 - 10 10 chr22 9816457 9825238 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6612348 | 6614881 | a | 0 | + | | chr1 | 51342 | 61311 | a | 0 | - | | chr2 | 51342 | 51544 | a | 0 | - | | chr2 | 7607576 | 7616894 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 9467564 | 9477523 | a | 0 | - | | chr15 | 3130547 | 3138411 | a | 0 | - | | chr19 | 4480036 | 4482016 | a | 0 | - | | chr22 | 9816457 | 9825238 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5077454 | 5079025 | a | 0 | + | | chr1 | 5393649 | 5393650 | a | 0 | + | | chr1 | 5393649 | 5394466 | a | 0 | - | | chr5 | 5393649 | 5394881 | a | 0 | - | | chr10 | 9564193 | 9565359 | a | 0 | - | | chr15 | 9756570 | 9761811 | a | 0 | + | | chr15 | 5943125 | 5949229 | a | 0 | + | | chrM | 5393649 | 5397389 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpe7vn5e6n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5077454 5079025 a 0 + 1 1 chr1 5393649 5393650 a 0 + 2 2 chr1 5393649 5394466 a 0 - 3 3 chr10 9564193 9565359 a 0 - 4 4 chr15 5943125 5949229 a 0 + 5 5 chr15 9756570 9761811 a 0 + 6 6 chr5 5393649 5394881 a 0 - 7 7 chrM 5393649 5397389 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5077454 | 5079025 | a | 0 | + | | chr1 | 5393649 | 5393650 | a | 0 | + | | chr1 | 5393649 | 5394466 | a | 0 | - | | chr5 | 5393649 | 5394881 | a | 0 | - | | chr10 | 9564193 | 9565359 | a | 0 | - | | chr15 | 9756570 | 9761811 | a | 0 | + | | chr15 | 5943125 | 5949229 | a | 0 | + | | chrM | 5393649 | 5397389 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3546327 | 3548131 | a | 0 | + | | chr1 | 9879010 | 9885063 | a | 0 | + | | chr1 | 471693 | 471873 | a | 0 | - | | chr11 | 8574991 | 8576018 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr21 | 9414673 | 9417748 | a | 0 | - | | chr22 | 1612489 | 1615564 | a | 0 | - | | chrX | 5547166 | 5555292 | a | 0 | - | | chrY | 9108502 | 9116358 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpkjm_d0yk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3546327 3548131 a 0 + 1 1 chr1 9879010 9885063 a 0 + 2 2 chr1 471693 471873 a 0 - 3 3 chr11 8574991 8576018 a 0 - 4 4 chr16 9408652 9418651 a 0 - 5 5 chr18 204571 214570 a 0 - 6 6 chr21 9414673 9417748 a 0 - 7 7 chr22 1612489 1615564 a 0 - 8 8 chrX 5547166 5555292 a 0 - 9 9 chrY 9108502 9116358 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3546327 | 3548131 | a | 0 | + | | chr1 | 9879010 | 9885063 | a | 0 | + | | chr1 | 471693 | 471873 | a | 0 | - | | chr11 | 8574991 | 8576018 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr21 | 9414673 | 9417748 | a | 0 | - | | chr22 | 1612489 | 1615564 | a | 0 | - | | chrX | 5547166 | 5555292 | a | 0 | - | | chrY | 9108502 | 9116358 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrM | 2664553 | 2669250 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpk52y29r1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chrM 2664553 2669250 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrM | 2664553 | 2669250 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 693138 | 697209 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpatd4uecx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 693138 697209 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 693138 | 697209 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9352246 | 9354208 | a | 0 | + | | chr1 | 5390798 | 5392760 | a | 0 | + | | chr1 | 9039673 | 9039963 | a | 0 | + | | chr1 | 3480912 | 3490499 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 2032463 | 2039821 | a | 0 | + | | chr8 | 3673311 | 3674554 | a | 0 | + | | chr11 | 2380312 | 2381380 | a | 0 | - | | chrM | 4721872 | 4726993 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpvsiiwias/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5390798 5392760 a 0 + 1 1 chr1 9039673 9039963 a 0 + 2 2 chr1 9352246 9354208 a 0 + 3 3 chr1 2916143 2918105 a 0 - 4 4 chr1 3480912 3490499 a 0 - 5 5 chr1 8612741 8620661 a 0 - 6 6 chr1 9664111 9668603 a 0 - 7 7 chr11 2380312 2381380 a 0 - 8 8 chr4 2032463 2039821 a 0 + 9 9 chr8 3673311 3674554 a 0 + 10 10 chrM 4721872 4726993 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9352246 | 9354208 | a | 0 | + | | chr1 | 5390798 | 5392760 | a | 0 | + | | chr1 | 9039673 | 9039963 | a | 0 | + | | chr1 | 3480912 | 3490499 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 2032463 | 2039821 | a | 0 | + | | chr8 | 3673311 | 3674554 | a | 0 | + | | chr11 | 2380312 | 2381380 | a | 0 | - | | chrM | 4721872 | 4726993 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 840923 | 845979 | a | 0 | + | | chr1 | 840923 | 845979 | a | 0 | + | | chr1 | 840923 | 842753 | a | 0 | + | | chr1 | 7933899 | 7943535 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 840923 | 850923 | a | 0 | + | | chr11 | 4342253 | 4347309 | a | 0 | + | | chr17 | 840923 | 850801 | a | 0 | + | | chr21 | 840923 | 842656 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmper0isi8r/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 840923 842753 a 0 + 1 1 chr1 840923 845979 a 0 + 1 2 chr1 840923 845979 a 0 + 1 3 chr1 840923 846639 a 0 - 2 4 chr1 5668554 5669352 a 0 - 3 5 chr1 7933899 7943535 a 0 - 4 6 chr11 4342253 4347309 a 0 + 5 7 chr17 840923 850801 a 0 + 6 8 chr21 840923 842656 a 0 + 7 9 chr4 840923 845460 a 0 - 8 10 chr7 840923 850923 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 840923 | 845979 | a | 0 | + | | chr1 | 840923 | 845979 | a | 0 | + | | chr1 | 840923 | 842753 | a | 0 | + | | chr1 | 7933899 | 7943535 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 840923 | 850923 | a | 0 | + | | chr11 | 4342253 | 4347309 | a | 0 | + | | chr17 | 840923 | 850801 | a | 0 | + | | chr21 | 840923 | 842656 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8100813 | 8108956 | a | 0 | - | | chr9 | 8100813 | 8109549 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpi2jnfk9r/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8100813 8108956 a 0 - 1 1 chr9 8100813 8109549 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8100813 | 8108956 | a | 0 | - | | chr9 | 8100813 | 8109549 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3986652 | 3991742 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpz5rnp40y/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3986652 3991742 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3986652 | 3991742 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5698543 | 5703004 | a | 0 | - | | chr1 | 6314956 | 6318480 | a | 0 | - | | chr1 | 4311818 | 4318693 | a | 0 | - | | chr9 | 5698543 | 5700930 | a | 0 | - | | chr11 | 1237353 | 1243419 | a | 0 | + | | chr15 | 5698543 | 5708543 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpc_lzqi5b/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4311818 4318693 a 0 - 1 1 chr1 5698543 5703004 a 0 - 2 2 chr1 6314956 6318480 a 0 - 3 3 chr11 1237353 1243419 a 0 + 4 4 chr15 5698543 5708543 a 0 - 5 5 chr9 5698543 5700930 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5698543 | 5703004 | a | 0 | - | | chr1 | 6314956 | 6318480 | a | 0 | - | | chr1 | 4311818 | 4318693 | a | 0 | - | | chr9 | 5698543 | 5700930 | a | 0 | - | | chr11 | 1237353 | 1243419 | a | 0 | + | | chr15 | 5698543 | 5708543 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10000036 | a | 0 | - | | chr1 | 6285615 | 6290446 | a | 0 | - | | chr8 | 9501162 | 9502605 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmprapcpg51/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6285615 6290446 a 0 - 1 1 chr1 9999999 10000036 a 0 - 2 2 chr8 9501162 9502605 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10000036 | a | 0 | - | | chr1 | 6285615 | 6290446 | a | 0 | - | | chr8 | 9501162 | 9502605 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4192968 | 4196319 | a | 0 | + | | chrX | 7067019 | 7068795 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdunko8lj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4192968 4196319 a 0 + 1 1 chrX 7067019 7068795 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4192968 | 4196319 | a | 0 | + | | chrX | 7067019 | 7068795 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7030991 | 7033163 | a | 0 | + | | chr14 | 2595510 | 2597488 | a | 0 | + | | chr20 | 9992791 | 10002433 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmphoh1tuwt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7030991 7033163 a 0 + 1 1 chr14 2595510 2597488 a 0 + 2 2 chr20 9992791 10002433 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7030991 | 7033163 | a | 0 | + | | chr14 | 2595510 | 2597488 | a | 0 | + | | chr20 | 9992791 | 10002433 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4495171 | 4504239 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpm5vr22vz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4495171 4504239 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4495171 | 4504239 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8989837 | 8994499 | a | 0 | + | | chr1 | 8832393 | 8837269 | a | 0 | + | | chr1 | 8989837 | 8994571 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpow7a7dp2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8832393 8837269 a 0 + 1 1 chr1 8989837 8994499 a 0 + 2 2 chr1 8989837 8994571 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8989837 | 8994499 | a | 0 | + | | chr1 | 8832393 | 8837269 | a | 0 | + | | chr1 | 8989837 | 8994571 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6240988 | 6248369 | a | 0 | - | | chr2 | 5259831 | 5264823 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpk41iuewy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6240988 6248369 a 0 - 1 1 chr2 5259831 5264823 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6240988 | 6248369 | a | 0 | - | | chr2 | 5259831 | 5264823 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 9698744 | 9702620 | a | 0 | - | | chr16 | 7372833 | 7382818 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxpswlo6m/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr16 7372833 7382818 a 0 - 1 1 chr7 9698744 9702620 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 9698744 | 9702620 | a | 0 | - | | chr16 | 7372833 | 7382818 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5622521 | 5627007 | a | 0 | - | | chr1 | 5780135 | 5785431 | a | 0 | - | | chr1 | 6916031 | 6916826 | a | 0 | - | | chr2 | 3149102 | 3158447 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 3070355 | 3073753 | a | 0 | + | | chr7 | 9877618 | 9879251 | a | 0 | - | | chr12 | 7455288 | 7462689 | a | 0 | + | | chrY | 4496219 | 4503508 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpgzzyz8i_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5622521 5627007 a 0 - 1 1 chr1 5780135 5785431 a 0 - 2 2 chr1 6916031 6916826 a 0 - 3 3 chr12 7455288 7462689 a 0 + 4 4 chr2 3149102 3158447 a 0 + 5 5 chr4 8868178 8868180 a 0 + 6 6 chr5 8171740 8179524 a 0 + 7 7 chr6 3070355 3073753 a 0 + 8 8 chr7 9877618 9879251 a 0 - 9 9 chrY 4496219 4503508 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5622521 | 5627007 | a | 0 | - | | chr1 | 5780135 | 5785431 | a | 0 | - | | chr1 | 6916031 | 6916826 | a | 0 | - | | chr2 | 3149102 | 3158447 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 3070355 | 3073753 | a | 0 | + | | chr7 | 9877618 | 9879251 | a | 0 | - | | chr12 | 7455288 | 7462689 | a | 0 | + | | chrY | 4496219 | 4503508 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1385706 | 1385954 | a | 0 | + | | chr1 | 8965195 | 8972077 | a | 0 | + | | chr1 | 830935 | 837265 | a | 0 | + | | chr7 | 7424650 | 7433567 | a | 0 | - | | chr17 | 1385706 | 1389123 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpvysac594/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 830935 837265 a 0 + 1 1 chr1 1385706 1385954 a 0 + 2 2 chr1 8965195 8972077 a 0 + 3 3 chr17 1385706 1389123 a 0 - 4 4 chr7 7424650 7433567 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1385706 | 1385954 | a | 0 | + | | chr1 | 8965195 | 8972077 | a | 0 | + | | chr1 | 830935 | 837265 | a | 0 | + | | chr7 | 7424650 | 7433567 | a | 0 | - | | chr17 | 1385706 | 1389123 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9161377 | 9161378 | a | 0 | - | | chr6 | 9489978 | 9498492 | a | 0 | + | | chr6 | 10000000 | 10006096 | a | 0 | - | | chr6 | 1569348 | 1578702 | a | 0 | - | | chr6 | 1390107 | 1400107 | a | 0 | - | | chr6 | 2878087 | 2885772 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpb_e8jh8o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9161377 9161378 a 0 - 1 1 chr6 9489978 9498492 a 0 + 2 2 chr6 1390107 1400107 a 0 - 3 3 chr6 1569348 1578702 a 0 - 4 4 chr6 2878087 2885772 a 0 - 5 5 chr6 10000000 10006096 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9161377 | 9161378 | a | 0 | - | | chr6 | 9489978 | 9498492 | a | 0 | + | | chr6 | 10000000 | 10006096 | a | 0 | - | | chr6 | 1569348 | 1578702 | a | 0 | - | | chr6 | 1390107 | 1400107 | a | 0 | - | | chr6 | 2878087 | 2885772 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7859050 | 7867864 | a | 0 | + | | chr1 | 7859050 | 7867885 | a | 0 | + | | chr1 | 7859050 | 7865615 | a | 0 | + | | chr1 | 7859050 | 7863453 | a | 0 | - | | chr10 | 7859050 | 7866798 | a | 0 | - | | chr17 | 7859050 | 7860471 | a | 0 | - | | chr20 | 7859050 | 7861331 | a | 0 | - | | chr21 | 7859050 | 7862292 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp3dfb9zsz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7859050 7865615 a 0 + 1 1 chr1 7859050 7867864 a 0 + 1 2 chr1 7859050 7867885 a 0 + 1 3 chr1 7859050 7863453 a 0 - 2 4 chr10 7859050 7866798 a 0 - 3 5 chr17 7859050 7860471 a 0 - 4 6 chr20 7859050 7861331 a 0 - 5 7 chr21 7859050 7862292 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7859050 | 7867864 | a | 0 | + | | chr1 | 7859050 | 7867885 | a | 0 | + | | chr1 | 7859050 | 7865615 | a | 0 | + | | chr1 | 7859050 | 7863453 | a | 0 | - | | chr10 | 7859050 | 7866798 | a | 0 | - | | chr17 | 7859050 | 7860471 | a | 0 | - | | chr20 | 7859050 | 7861331 | a | 0 | - | | chr21 | 7859050 | 7862292 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3979860 | 3988837 | a | 0 | + | | chr3 | 6494183 | 6495624 | a | 0 | - | | chr5 | 7059149 | 7061297 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpc8inchzj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3979860 3988837 a 0 + 1 1 chr3 6494183 6495624 a 0 - 2 2 chr5 7059149 7061297 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3979860 | 3988837 | a | 0 | + | | chr3 | 6494183 | 6495624 | a | 0 | - | | chr5 | 7059149 | 7061297 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3674 | a | 0 | + | | chr1 | 5079716 | 5080033 | a | 0 | + | | chr1 | 2439700 | 2442970 | a | 0 | - | | chr1 | 1 | 7472 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 993071 | 999317 | a | 0 | - | | chr1 | 6933132 | 6935186 | a | 0 | - | | chr1 | 6329580 | 6331204 | a | 0 | - | | chr1 | 393659 | 400800 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7wiyc43f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 3674 a 0 + 1 1 chr1 5079716 5080033 a 0 + 2 2 chr1 1 7472 a 0 - 3 3 chr1 393659 400800 a 0 - 4 4 chr1 993071 999317 a 0 - 5 5 chr1 1256726 1261681 a 0 - 6 6 chr1 2439700 2442970 a 0 - 7 7 chr1 6329580 6331204 a 0 - 8 8 chr1 6661269 6663065 a 0 - 9 9 chr1 6933132 6935186 a 0 - 10 10 chr1 7323502 7324544 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3674 | a | 0 | + | | chr1 | 5079716 | 5080033 | a | 0 | + | | chr1 | 2439700 | 2442970 | a | 0 | - | | chr1 | 1 | 7472 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 993071 | 999317 | a | 0 | - | | chr1 | 6933132 | 6935186 | a | 0 | - | | chr1 | 6329580 | 6331204 | a | 0 | - | | chr1 | 393659 | 400800 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7772525 | 7777385 | a | 0 | + | | chr1 | 2158136 | 2164636 | a | 0 | + | | chr1 | 1673685 | 1677328 | a | 0 | - | | chr1 | 2990208 | 2995613 | a | 0 | - | | chr12 | 9426477 | 9428529 | a | 0 | - | | chr21 | 1092306 | 1099262 | a | 0 | + | | chr22 | 3467452 | 3474408 | a | 0 | + | | chr22 | 2939094 | 2946050 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp4hfkqyn0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2158136 2164636 a 0 + 1 1 chr1 7772525 7777385 a 0 + 2 2 chr1 1673685 1677328 a 0 - 3 3 chr1 2990208 2995613 a 0 - 4 4 chr12 9426477 9428529 a 0 - 5 5 chr21 1092306 1099262 a 0 + 6 6 chr22 3467452 3474408 a 0 + 7 7 chr22 2939094 2946050 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7772525 | 7777385 | a | 0 | + | | chr1 | 2158136 | 2164636 | a | 0 | + | | chr1 | 1673685 | 1677328 | a | 0 | - | | chr1 | 2990208 | 2995613 | a | 0 | - | | chr12 | 9426477 | 9428529 | a | 0 | - | | chr21 | 1092306 | 1099262 | a | 0 | + | | chr22 | 3467452 | 3474408 | a | 0 | + | | chr22 | 2939094 | 2946050 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1213830 | 1218639 | a | 0 | + | | chr1 | 5714862 | 5719722 | a | 0 | + | | chr1 | 4880053 | 4881495 | a | 0 | + | | chr1 | 7438817 | 7441286 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 5017325 | 5025030 | a | 0 | + | | chr14 | 8426664 | 8427912 | a | 0 | - | | chr18 | 6991509 | 6999094 | a | 0 | + | | chr19 | 3137983 | 3142724 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdnrp0xk1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1213830 1218639 a 0 + 1 1 chr1 4880053 4881495 a 0 + 2 2 chr1 5714862 5719722 a 0 + 3 3 chr1 7438817 7441286 a 0 - 4 4 chr14 5017325 5025030 a 0 + 5 5 chr14 8426664 8427912 a 0 - 6 6 chr18 6991509 6999094 a 0 + 7 7 chr19 3137983 3142724 a 0 - 8 8 chr5 6230212 6234196 a 0 + 9 9 chr6 7878102 7888102 a 0 + 10 10 chrM 8680820 8683958 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1213830 | 1218639 | a | 0 | + | | chr1 | 5714862 | 5719722 | a | 0 | + | | chr1 | 4880053 | 4881495 | a | 0 | + | | chr1 | 7438817 | 7441286 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 5017325 | 5025030 | a | 0 | + | | chr14 | 8426664 | 8427912 | a | 0 | - | | chr18 | 6991509 | 6999094 | a | 0 | + | | chr19 | 3137983 | 3142724 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3414949 | 3416470 | a | 0 | + | | chr3 | 8316597 | 8325591 | a | 0 | + | | chr3 | 1762210 | 1764168 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7aji0pzb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3414949 3416470 a 0 + 1 1 chr3 8316597 8325591 a 0 + 2 2 chr3 1762210 1764168 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3414949 | 3416470 | a | 0 | + | | chr3 | 8316597 | 8325591 | a | 0 | + | | chr3 | 1762210 | 1764168 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8095637 | 8101593 | a | 0 | - | | chr1 | 6690318 | 6695118 | a | 0 | - | | chr1 | 3321817 | 3330012 | a | 0 | - | | chr1 | 54758 | 64757 | a | 0 | - | | chr4 | 3961095 | 3964951 | a | 0 | - | | chrX | 7552171 | 7557197 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpvsmi_5w3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 54758 64757 a 0 - 1 1 chr1 3321817 3330012 a 0 - 2 2 chr1 6690318 6695118 a 0 - 3 3 chr1 8095637 8101593 a 0 - 4 4 chr4 3961095 3964951 a 0 - 5 5 chrX 7552171 7557197 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8095637 | 8101593 | a | 0 | - | | chr1 | 6690318 | 6695118 | a | 0 | - | | chr1 | 3321817 | 3330012 | a | 0 | - | | chr1 | 54758 | 64757 | a | 0 | - | | chr4 | 3961095 | 3964951 | a | 0 | - | | chrX | 7552171 | 7557197 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10004874 | a | 0 | + | | chr1 | 5194958 | 5200895 | a | 0 | + | | chr1 | 635934 | 641871 | a | 0 | + | | chr1 | 843791 | 849728 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 728109 | 734046 | a | 0 | - | | chr17 | 7541474 | 7546919 | a | 0 | + | | chrM | 2217067 | 2223004 | a | 0 | - | | chrY | 3031439 | 3037376 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmybpcm31/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 635934 641871 a 0 + 1 1 chr1 5194958 5200895 a 0 + 2 2 chr1 10000000 10004874 a 0 + 3 3 chr1 843791 849728 a 0 - 4 4 chr1 3172329 3176746 a 0 - 5 5 chr1 3908014 3913951 a 0 - 6 6 chr17 7541474 7546919 a 0 + 7 7 chr6 4199766 4200758 a 0 + 8 8 chr7 728109 734046 a 0 - 9 9 chrM 2217067 2223004 a 0 - 10 10 chrY 3031439 3037376 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10004874 | a | 0 | + | | chr1 | 5194958 | 5200895 | a | 0 | + | | chr1 | 635934 | 641871 | a | 0 | + | | chr1 | 843791 | 849728 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 728109 | 734046 | a | 0 | - | | chr17 | 7541474 | 7546919 | a | 0 | + | | chrM | 2217067 | 2223004 | a | 0 | - | | chrY | 3031439 | 3037376 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 10000000 | 10002811 | a | 0 | + | | chr11 | 4741801 | 4743269 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpsnu3nv_0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr11 10000000 10002811 a 0 + 1 1 chr11 4741801 4743269 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 10000000 | 10002811 | a | 0 | + | | chr11 | 4741801 | 4743269 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1687184 | 1695060 | a | 0 | + | | chr1 | 2121700 | 2129576 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpre4hsn1s/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1687184 1695060 a 0 + 1 1 chr1 2121700 2129576 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1687184 | 1695060 | a | 0 | + | | chr1 | 2121700 | 2129576 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3096044 | 3103065 | a | 0 | + | | chr1 | 5876264 | 5879157 | a | 0 | + | | chr1 | 2231481 | 2232704 | a | 0 | + | | chr1 | 5306467 | 5316467 | a | 0 | - | | chr1 | 5306467 | 5306468 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp52r1q2fi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2231481 2232704 a 0 + 1 1 chr1 3096044 3103065 a 0 + 2 2 chr1 5876264 5879157 a 0 + 3 3 chr1 5306467 5306468 a 0 - 4 4 chr1 5306467 5316467 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3096044 | 3103065 | a | 0 | + | | chr1 | 5876264 | 5879157 | a | 0 | + | | chr1 | 2231481 | 2232704 | a | 0 | + | | chr1 | 5306467 | 5316467 | a | 0 | - | | chr1 | 5306467 | 5306468 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6425763 | 6431121 | a | 0 | + | | chr1 | 3861918 | 3863634 | a | 0 | - | | chr1 | 2394605 | 2404557 | a | 0 | - | | chr1 | 5170530 | 5179416 | a | 0 | - | | chr7 | 8232007 | 8241191 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdczhglut/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6425763 6431121 a 0 + 1 1 chr1 2394605 2404557 a 0 - 2 2 chr1 3861918 3863634 a 0 - 3 3 chr1 5170530 5179416 a 0 - 4 4 chr7 8232007 8241191 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6425763 | 6431121 | a | 0 | + | | chr1 | 3861918 | 3863634 | a | 0 | - | | chr1 | 2394605 | 2404557 | a | 0 | - | | chr1 | 5170530 | 5179416 | a | 0 | - | | chr7 | 8232007 | 8241191 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4038910 | 4046535 | a | 0 | + | | chr1 | 5989565 | 5994642 | a | 0 | - | | chr12 | 6670245 | 6675853 | a | 0 | + | | chr17 | 4283899 | 4285506 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr17 | 687421 | 689069 | a | 0 | + | | chr17 | 5217058 | 5221129 | a | 0 | + | | chr17 | 1181979 | 1186064 | a | 0 | - | | chr17 | 9999999 | 10002365 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpp5fzp_nd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4038910 4046535 a 0 + 1 1 chr1 5989565 5994642 a 0 - 2 2 chr12 6670245 6675853 a 0 + 3 3 chr17 687421 689069 a 0 + 4 4 chr17 4283899 4285506 a 0 + 5 5 chr17 5217058 5221129 a 0 + 6 6 chr17 5359395 5361136 a 0 + 7 7 chr17 1181979 1186064 a 0 - 8 8 chr17 9999999 10002365 a 0 - 9 9 chr22 1064343 1069540 a 0 + 10 10 chrX 1461780 1466976 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4038910 | 4046535 | a | 0 | + | | chr1 | 5989565 | 5994642 | a | 0 | - | | chr12 | 6670245 | 6675853 | a | 0 | + | | chr17 | 4283899 | 4285506 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr17 | 687421 | 689069 | a | 0 | + | | chr17 | 5217058 | 5221129 | a | 0 | + | | chr17 | 1181979 | 1186064 | a | 0 | - | | chr17 | 9999999 | 10002365 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2534672 | 2535519 | a | 0 | + | | chr1 | 4576478 | 4585525 | a | 0 | + | | chr1 | 5881636 | 5885469 | a | 0 | - | | chr1 | 717392 | 723739 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr21 | 9952077 | 9955910 | a | 0 | + | | chrM | 9999999 | 10003832 | a | 0 | - | | chrX | 1333700 | 1339831 | a | 0 | + | | chrX | 4463849 | 4464653 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp6lj29fy9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2534672 2535519 a 0 + 1 1 chr1 4576478 4585525 a 0 + 2 2 chr1 717392 723739 a 0 - 3 3 chr1 5881636 5885469 a 0 - 4 4 chr13 5988746 5990831 a 0 - 5 5 chr15 213024 213025 a 0 - 6 6 chr21 9952077 9955910 a 0 + 7 7 chrM 9999999 10003832 a 0 - 8 8 chrX 1333700 1339831 a 0 + 9 9 chrX 4463849 4464653 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2534672 | 2535519 | a | 0 | + | | chr1 | 4576478 | 4585525 | a | 0 | + | | chr1 | 5881636 | 5885469 | a | 0 | - | | chr1 | 717392 | 723739 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr21 | 9952077 | 9955910 | a | 0 | + | | chrM | 9999999 | 10003832 | a | 0 | - | | chrX | 1333700 | 1339831 | a | 0 | + | | chrX | 4463849 | 4464653 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1061286 | 1066242 | a | 0 | + | | chr4 | 2280491 | 2286902 | a | 0 | + | | chr10 | 2015861 | 2021882 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5_1tb6bb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1061286 1066242 a 0 + 1 1 chr10 2015861 2021882 a 0 + 2 2 chr4 2280491 2286902 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1061286 | 1066242 | a | 0 | + | | chr4 | 2280491 | 2286902 | a | 0 | + | | chr10 | 2015861 | 2021882 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6607431 | 6607503 | a | 0 | + | | chr1 | 5425558 | 5426901 | a | 0 | + | | chr1 | 9680921 | 9686898 | a | 0 | - | | chr1 | 8402147 | 8411718 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 2092658 | 2099352 | a | 0 | - | | chr15 | 2797022 | 2803144 | a | 0 | - | | chr17 | 1238734 | 1244684 | a | 0 | + | | chr22 | 2239521 | 2248437 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2vev_qaj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5425558 5426901 a 0 + 1 1 chr1 6607431 6607503 a 0 + 2 2 chr1 8402147 8411718 a 0 - 3 3 chr1 9680921 9686898 a 0 - 4 4 chr1 9999999 10002329 a 0 - 5 5 chr11 2092658 2099352 a 0 - 6 6 chr15 2797022 2803144 a 0 - 7 7 chr17 1238734 1244684 a 0 + 8 8 chr22 2239521 2248437 a 0 - 9 9 chr3 1516990 1522222 a 0 - 10 10 chr4 1516990 1525549 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6607431 | 6607503 | a | 0 | + | | chr1 | 5425558 | 5426901 | a | 0 | + | | chr1 | 9680921 | 9686898 | a | 0 | - | | chr1 | 8402147 | 8411718 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 2092658 | 2099352 | a | 0 | - | | chr15 | 2797022 | 2803144 | a | 0 | - | | chr17 | 1238734 | 1244684 | a | 0 | + | | chr22 | 2239521 | 2248437 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1473550 | 1479609 | a | 0 | + | | chr1 | 9870850 | 9879466 | a | 0 | - | | chr2 | 2596416 | 2605864 | a | 0 | + | | chr7 | 7741249 | 7750441 | a | 0 | - | | chr22 | 1328129 | 1329710 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmppjfz_8nz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1473550 1479609 a 0 + 1 1 chr1 9870850 9879466 a 0 - 2 2 chr2 2596416 2605864 a 0 + 3 3 chr22 1328129 1329710 a 0 - 4 4 chr7 7741249 7750441 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1473550 | 1479609 | a | 0 | + | | chr1 | 9870850 | 9879466 | a | 0 | - | | chr2 | 2596416 | 2605864 | a | 0 | + | | chr7 | 7741249 | 7750441 | a | 0 | - | | chr22 | 1328129 | 1329710 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4190071 | 4196580 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpw09is8g9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4190071 4196580 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4190071 | 4196580 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6130645 | 6132579 | a | 0 | + | | chr1 | 4096358 | 4104311 | a | 0 | - | | chr1 | 9477563 | 9484202 | a | 0 | - | | chr8 | 7006428 | 7006429 | a | 0 | + | | chr12 | 4128187 | 4130125 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpsgrq3ddp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6130645 6132579 a 0 + 1 1 chr1 4096358 4104311 a 0 - 2 2 chr1 9477563 9484202 a 0 - 3 3 chr12 4128187 4130125 a 0 - 4 4 chr8 7006428 7006429 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6130645 | 6132579 | a | 0 | + | | chr1 | 4096358 | 4104311 | a | 0 | - | | chr1 | 9477563 | 9484202 | a | 0 | - | | chr8 | 7006428 | 7006429 | a | 0 | + | | chr12 | 4128187 | 4130125 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4439261 | 4439455 | a | 0 | + | | chr1 | 10000000 | 10005209 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5bt7m8bp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4439261 4439455 a 0 + 1 1 chr1 10000000 10005209 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4439261 | 4439455 | a | 0 | + | | chr1 | 10000000 | 10005209 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7908752 | 7908754 | a | 0 | + | | chr1 | 2627847 | 2630101 | a | 0 | - | | chr1 | 9920779 | 9928630 | a | 0 | - | | chr1 | 9806660 | 9814894 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 47925 | 52374 | a | 0 | + | | chr9 | 4179468 | 4180841 | a | 0 | + | | chr13 | 6413277 | 6420489 | a | 0 | + | | chr13 | 4947897 | 4957554 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpn5j3muhy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7908752 7908754 a 0 + 1 1 chr1 2627847 2630101 a 0 - 2 2 chr1 9806660 9814894 a 0 - 3 3 chr1 9920779 9928630 a 0 - 4 4 chr13 6413277 6420489 a 0 + 5 5 chr13 4947897 4957554 a 0 - 6 6 chr9 47925 52374 a 0 + 7 7 chr9 4179468 4180841 a 0 + 8 8 chrM 4941831 4948510 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7908752 | 7908754 | a | 0 | + | | chr1 | 2627847 | 2630101 | a | 0 | - | | chr1 | 9920779 | 9928630 | a | 0 | - | | chr1 | 9806660 | 9814894 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 47925 | 52374 | a | 0 | + | | chr9 | 4179468 | 4180841 | a | 0 | + | | chr13 | 6413277 | 6420489 | a | 0 | + | | chr13 | 4947897 | 4957554 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp12je91d_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ______________________________ test_merge[False] _______________________________ [gw1] linux -- Python 3.12.2 /usr/bin/python3.12 strand = False @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:31: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:75: in test_merge result = gr.merge(strand=strand, count=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_merge( E strand=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_dpxxexx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3222880 | 3231141 | a | 0 | + | | chr1 | 5760670 | 5764252 | a | 0 | + | | chr1 | 8159063 | 8161294 | a | 0 | + | | chr1 | 8810136 | 8818030 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpa17vewsx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3222880 3231141 + 1 chr1 5760670 5764252 + 1 chr1 8159063 8161294 + 1 chr1 8810136 8818030 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3222880 3231141 1 1 chr1 5760670 5764252 1 2 chr1 8159063 8161294 1 3 chr1 8810136 8818030 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3222880 | 3231141 | a | 0 | + | | chr1 | 5760670 | 5764252 | a | 0 | + | | chr1 | 8159063 | 8161294 | a | 0 | + | | chr1 | 8810136 | 8818030 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_uz9zluf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3222880 3231141 + 1 chr1 5760670 5764252 + 1 chr1 8159063 8161294 + 1 chr1 8810136 8818030 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3222880 3231141 1 1 chr1 5760670 5764252 1 2 chr1 8159063 8161294 1 3 chr1 8810136 8818030 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65794 | 65908 | a | 0 | + | | chr1 | 1966357 | 1970200 | a | 0 | + | | chr1 | 77838 | 81681 | a | 0 | - | | chr1 | 851969 | 855812 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpsaxzryim/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 65794 65908 + 1 chr1 77838 81681 - 1 chr1 851969 855812 - 1 chr1 1966357 1970200 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 65794 65908 1 1 chr1 77838 81681 1 2 chr1 851969 855812 1 3 chr1 1966357 1970200 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65794 | 69380 | a | 0 | + | | chr1 | 851969 | 855298 | a | 0 | + | | chr1 | 1966357 | 1974039 | a | 0 | - | | chr1 | 77838 | 81168 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp47n8cpwa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 65794 69380 + 1 chr1 77838 81168 - 1 chr1 851969 855298 + 1 chr1 1966357 1974039 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 65794 69380 1 1 chr1 77838 81168 1 2 chr1 851969 855298 1 3 chr1 1966357 1974039 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65794 | 69380 | a | 0 | + | | chr1 | 851969 | 855298 | a | 0 | + | | chr1 | 1966357 | 1974039 | a | 0 | - | | chr1 | 77838 | 81168 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpjwjgh7az/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 65794 69380 + 1 chr1 77838 81168 - 1 chr1 851969 855298 + 1 chr1 1966357 1974039 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 65794 69380 1 1 chr1 77838 81168 1 2 chr1 851969 855298 1 3 chr1 1966357 1974039 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65794 | 69380 | a | 0 | + | | chr1 | 851969 | 855298 | a | 0 | + | | chr1 | 1966357 | 1974039 | a | 0 | - | | chr1 | 77838 | 81168 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3erwya2n/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 65794 69380 + 1 chr1 77838 81168 - 1 chr1 851969 855298 + 1 chr1 1966357 1974039 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 65794 69380 1 1 chr1 77838 81168 1 2 chr1 851969 855298 1 3 chr1 1966357 1974039 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65794 | 69380 | a | 0 | + | | chr1 | 851969 | 855298 | a | 0 | + | | chr1 | 1966357 | 1974039 | a | 0 | - | | chr1 | 77838 | 81168 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpwjiufny3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 65794 69380 + 1 chr1 77838 81168 - 1 chr1 851969 855298 + 1 chr1 1966357 1974039 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 65794 69380 1 1 chr1 77838 81168 1 2 chr1 851969 855298 1 3 chr1 1966357 1974039 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9820047 | 9820276 | a | 0 | + | | chr3 | 2654340 | 2663294 | a | 0 | + | | chr3 | 5826441 | 5832457 | a | 0 | - | | chr3 | 9171512 | 9177415 | a | 0 | - | | chr4 | 5706734 | 5712141 | a | 0 | - | | chr12 | 1570627 | 1570684 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpm0spmgop/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9820047 9820276 + 1 chr12 1570627 1570684 - 1 chr3 2654340 2663294 + 1 chr3 5826441 5832457 - 1 chr3 9171512 9177415 - 1 chr4 5706734 5712141 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9820047 9820276 1 1 chr12 1570627 1570684 1 2 chr3 2654340 2663294 1 3 chr3 5826441 5832457 1 4 chr3 9171512 9177415 1 5 chr4 5706734 5712141 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9820047 | 9820276 | a | 0 | - | | chr3 | 5826441 | 5832457 | a | 0 | + | | chr3 | 9171512 | 9177415 | a | 0 | + | | chr3 | 2654340 | 2663294 | a | 0 | - | | chr4 | 5706734 | 5712141 | a | 0 | + | | chr12 | 1570627 | 1570684 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmplm5hvyhh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9820047 9820276 - 1 chr12 1570627 1570684 + 1 chr3 2654340 2663294 - 1 chr3 5826441 5832457 + 1 chr3 9171512 9177415 + 1 chr4 5706734 5712141 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9820047 9820276 1 1 chr12 1570627 1570684 1 2 chr3 2654340 2663294 1 3 chr3 5826441 5832457 1 4 chr3 9171512 9177415 1 5 chr4 5706734 5712141 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpyo4icl3c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpllxaw8c4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmps7y_nppe/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpnqj0pudo/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3r7p0g0b/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpr87tpys3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpzip5hhde/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmphsrqkmvf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpufxcs2ft/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp72n7qsdr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpq1rtlabf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpqk7xntzt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8369899 | 8378169 | a | 0 | + | | chr1 | 2495650 | 2503290 | a | 0 | + | | chr1 | 6458323 | 6459677 | a | 0 | - | | chr1 | 4446484 | 4446486 | a | 0 | - | | chrY | 4924080 | 4931720 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpefs377zr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2495650 2503290 + 1 chr1 4446484 4446486 - 1 chr1 6458323 6459677 - 1 chr1 8369899 8378169 + 1 chrY 4924080 4931720 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2495650 2503290 1 1 chr1 4446484 4446486 1 2 chr1 6458323 6459677 1 3 chr1 8369899 8378169 1 4 chrY 4924080 4931720 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7893026 | 7897081 | a | 0 | + | | chr1 | 4215979 | 4217798 | a | 0 | - | | chr1 | 8536771 | 8543301 | a | 0 | - | | chr9 | 5673249 | 5674452 | a | 0 | - | | chr10 | 7463589 | 7465431 | a | 0 | - | | chr10 | 9740008 | 9743374 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpbg26tdjr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4215979 4217798 - 1 chr1 7893026 7897081 + 1 chr1 8536771 8543301 - 1 chr10 7463589 7465431 - 1 chr10 9740008 9743374 - 1 chr9 5673249 5674452 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4215979 4217798 1 1 chr1 7893026 7897081 1 2 chr1 8536771 8543301 1 3 chr10 7463589 7465431 1 4 chr10 9740008 9743374 1 5 chr9 5673249 5674452 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr18 | 9391381 | 9400050 | a | 0 | - | | chrX | 100491 | 103502 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpoel0r6go/f1.bed) resultresultresultresultresultresultresultresultresultresult chr18 9391381 9400050 - 1 chrX 100491 103502 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr18 9391381 9400050 1 1 chrX 100491 103502 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 2725105 | 2730770 | a | 0 | - | | chr12 | 5799096 | 5799769 | a | 0 | + | | chr14 | 7948729 | 7955693 | a | 0 | + | | chr16 | 417312 | 420403 | a | 0 | - | | chrY | 7585286 | 7593238 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8cz1yx01/f1.bed) resultresultresultresultresultresultresultresultresultresult chr12 5799096 5799769 + 1 chr14 7948729 7955693 + 1 chr16 417312 420403 - 1 chr6 2725105 2730770 - 1 chrY 7585286 7593238 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr12 5799096 5799769 1 1 chr14 7948729 7955693 1 2 chr16 417312 420403 1 3 chr6 2725105 2730770 1 4 chrY 7585286 7593238 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 3012644 | 3021881 | a | 0 | + | | chr10 | 5651292 | 5652024 | a | 0 | + | | chr10 | 3373679 | 3379163 | a | 0 | + | | chr10 | 1583823 | 1589162 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpd9sl1aou/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 1583823 1589162 - 1 chr10 3373679 3379163 + 1 chr10 5651292 5652024 + 1 chr8 3012644 3021881 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr10 1583823 1589162 1 1 chr10 3373679 3379163 1 2 chr10 5651292 5652024 1 3 chr8 3012644 3021881 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 5652 | a | 0 | + | | chr1 | 3777253 | 3777254 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmphrr62yct/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 5652 + 1 chr1 3777253 3777254 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2 5652 1 1 chr1 3777253 3777254 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3492533 | 3497223 | a | 0 | + | | chr1 | 2442935 | 2443449 | a | 0 | + | | chr1 | 6982646 | 6983492 | a | 0 | + | | chr1 | 9448286 | 9450181 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 8220 | a | 0 | + | | chr1 | 3777994 | 3783610 | a | 0 | + | | chr1 | 1 | 9819 | a | 0 | - | | chr1 | 770426 | 779457 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp343gsvme/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 9819 + 2 chr1 770426 779457 - 1 chr1 2442935 2443449 + 1 chr1 3492533 3497223 + 1 chr1 3777994 3783610 + 1 chr1 6982646 6983492 + 1 chr1 9448286 9450181 + 1 chr14 6429083 6435146 - 1 chr6 6337484 6343551 + 1 chrX 2816356 2817711 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 9819 2 1 chr1 770426 779457 1 2 chr1 2442935 2443449 1 3 chr1 3492533 3497223 1 4 chr1 3777994 3783610 1 5 chr1 6982646 6983492 1 6 chr1 9448286 9450181 1 7 chr14 6429083 6435146 1 8 chr6 6337484 6343551 1 9 chrX 2816356 2817711 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7237 | a | 0 | + | | chr1 | 8257175 | 8260529 | a | 0 | + | | chr1 | 4972295 | 4975649 | a | 0 | + | | chr1 | 2702300 | 2705654 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1418188 | 1421542 | a | 0 | - | | chr1 | 2786843 | 2790197 | a | 0 | - | | chr1 | 9443934 | 9449660 | a | 0 | - | | chr1 | 2318349 | 2321703 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpd8x45hc3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7237 + 1 chr1 1418188 1421542 - 1 chr1 2318349 2321703 - 1 chr1 2702300 2705654 + 1 chr1 2786843 2790197 - 1 chr1 4972295 4975649 + 1 chr1 8257175 8260529 + 1 chr1 9443934 9449660 - 1 chr2 8449800 8459408 - 1 chr5 3591772 3595593 + 1 chrX 4226588 4229942 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 7237 1 1 chr1 1418188 1421542 1 2 chr1 2318349 2321703 1 3 chr1 2702300 2705654 1 4 chr1 2786843 2790197 1 5 chr1 4972295 4975649 1 6 chr1 8257175 8260529 1 7 chr1 9443934 9449660 1 8 chr2 8449800 8459408 1 9 chr5 3591772 3595593 1 10 chrX 4226588 4229942 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 1227 | a | 0 | + | | chr1 | 9954209 | 9955434 | a | 0 | - | | chr1 | 5704809 | 5710611 | a | 0 | - | | chr1 | 6937304 | 6945558 | a | 0 | - | | chr10 | 1005218 | 1006443 | a | 0 | - | | chr11 | 370116 | 370118 | a | 0 | + | | chr12 | 813754 | 813788 | a | 0 | - | | chrY | 9678871 | 9687548 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpcl3toh0g/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 1227 + 1 chr1 5704809 5710611 - 1 chr1 6937304 6945558 - 1 chr1 9954209 9955434 - 1 chr10 1005218 1006443 - 1 chr11 370116 370118 + 1 chr12 813754 813788 - 1 chrY 9678871 9687548 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2 1227 1 1 chr1 5704809 5710611 1 2 chr1 6937304 6945558 1 3 chr1 9954209 9955434 1 4 chr10 1005218 1006443 1 5 chr11 370116 370118 1 6 chr12 813754 813788 1 7 chrY 9678871 9687548 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 9922910 | 9932631 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp7hcq14nk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr15 9922910 9932631 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr15 9922910 9932631 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6924562 | 6925824 | a | 0 | + | | chr1 | 5234398 | 5241824 | a | 0 | + | | chr1 | 5234398 | 5235033 | a | 0 | - | | chr2 | 5234398 | 5244398 | a | 0 | + | | chr10 | 9427509 | 9429589 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfro_0y4k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5234398 5241824 - 2 chr1 6924562 6925824 + 1 chr10 9427509 9429589 - 1 chr2 5234398 5244398 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5234398 5241824 2 1 chr1 6924562 6925824 1 2 chr10 9427509 9429589 1 3 chr2 5234398 5244398 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1030267 | 1032496 | a | 0 | + | | chr1 | 1513612 | 1520212 | a | 0 | - | | chr2 | 7152531 | 7154611 | a | 0 | + | | chr5 | 5800119 | 5802348 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfrozau7y/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1030267 1032496 + 1 chr1 1513612 1520212 - 1 chr2 7152531 7154611 + 1 chr5 5800119 5802348 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1030267 1032496 1 1 chr1 1513612 1520212 1 2 chr2 7152531 7154611 1 3 chr5 5800119 5802348 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4119318 | 4125205 | a | 0 | - | | chr1 | 8587377 | 8591597 | a | 0 | - | | chr1 | 5894303 | 5898315 | a | 0 | - | | chr4 | 7687104 | 7695614 | a | 0 | + | | chr15 | 9741266 | 9742245 | a | 0 | + | | chr16 | 7974892 | 7984597 | a | 0 | + | | chr19 | 7865156 | 7865439 | a | 0 | - | | chrY | 3571027 | 3576340 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp08gqre4s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4119318 4125205 - 1 chr1 5894303 5898315 - 1 chr1 8587377 8591597 - 1 chr15 9741266 9742245 + 1 chr16 7974892 7984597 + 1 chr19 7865156 7865439 - 1 chr4 7687104 7695614 + 1 chrY 3571027 3576340 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4119318 4125205 1 1 chr1 5894303 5898315 1 2 chr1 8587377 8591597 1 3 chr15 9741266 9742245 1 4 chr16 7974892 7984597 1 5 chr19 7865156 7865439 1 6 chr4 7687104 7695614 1 7 chrY 3571027 3576340 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6625162 | 6635143 | a | 0 | + | | chr1 | 2035782 | 2044100 | a | 0 | + | | chr1 | 2819943 | 2820280 | a | 0 | + | | chr1 | 906305 | 906835 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 3911741 | 3912924 | a | 0 | + | | chr8 | 1397324 | 1405560 | a | 0 | + | | chr13 | 8924539 | 8931681 | a | 0 | + | | chr17 | 1229397 | 1238466 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpmiinb2ee/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 906305 906835 + 1 chr1 1907920 1910336 - 1 chr1 2035782 2044100 + 1 chr1 2819943 2820280 + 1 chr1 6115881 6124682 - 1 chr1 6625162 6635143 + 1 chr13 8924539 8931681 + 1 chr17 1229397 1238466 + 1 chr6 3911741 3912924 + 1 chr8 1397324 1405560 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 906305 906835 1 1 chr1 1907920 1910336 1 2 chr1 2035782 2044100 1 3 chr1 2819943 2820280 1 4 chr1 6115881 6124682 1 5 chr1 6625162 6635143 1 6 chr13 8924539 8931681 1 7 chr17 1229397 1238466 1 8 chr6 3911741 3912924 1 9 chr8 1397324 1405560 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1387625 | 1397546 | a | 0 | + | | chr1 | 7331280 | 7331281 | a | 0 | + | | chr1 | 9529138 | 9537112 | a | 0 | + | | chr1 | 2138963 | 2144872 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 2718828 | 2719058 | a | 0 | + | | chr16 | 4302894 | 4309099 | a | 0 | + | | chr18 | 1081968 | 1091968 | a | 0 | - | | chrM | 9726024 | 9730957 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfkpebct4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1387625 1397546 + 1 chr1 2138963 2144872 - 1 chr1 7331280 7331281 + 1 chr1 9529138 9537112 + 1 chr11 2918450 2921746 - 1 chr13 3808892 3811292 + 1 chr15 2718828 2719058 + 1 chr16 4302894 4309099 + 1 chr18 1081968 1091968 - 1 chr8 9104068 9110744 - 1 chrM 9726024 9730957 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1387625 1397546 1 1 chr1 2138963 2144872 1 2 chr1 7331280 7331281 1 3 chr1 9529138 9537112 1 4 chr11 2918450 2921746 1 5 chr13 3808892 3811292 1 6 chr15 2718828 2719058 1 7 chr16 4302894 4309099 1 8 chr18 1081968 1091968 1 9 chr8 9104068 9110744 1 10 chrM 9726024 9730957 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5355196 | 5355197 | a | 0 | - | | chr19 | 5115 | 9880 | a | 0 | + | | chr19 | 3971727 | 3977770 | a | 0 | + | | chr19 | 6099814 | 6108545 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpxu5fjfvi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5355196 5355197 - 1 chr19 5115 9880 + 1 chr19 3971727 3977770 + 1 chr19 6099814 6108545 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5355196 5355197 1 1 chr19 5115 9880 1 2 chr19 3971727 3977770 1 3 chr19 6099814 6108545 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8911816 | 8917396 | a | 0 | + | | chr1 | 1 | 6586 | a | 0 | - | | chr8 | 10000000 | 10002661 | a | 0 | + | | chr8 | 9585147 | 9587136 | a | 0 | - | | chr11 | 8966087 | 8967082 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp255gc9ho/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 6586 - 1 chr1 8911816 8917396 + 1 chr11 8966087 8967082 - 1 chr8 9585147 9587136 - 1 chr8 10000000 10002661 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 6586 1 1 chr1 8911816 8917396 1 2 chr11 8966087 8967082 1 3 chr8 9585147 9587136 1 4 chr8 10000000 10002661 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr12 | 10000000 | 10004187 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpv5u5aj7p/f1.bed) resultresultresultresultresultresultresultresultresultresult chr12 10000000 10004187 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr12 10000000 10004187 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4330227 | 4333845 | a | 0 | - | | chr6 | 3251955 | 3257666 | a | 0 | - | | chr6 | 1817197 | 1824444 | a | 0 | - | | chr10 | 2711657 | 2717400 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9vqs4dah/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4330227 4333845 - 1 chr10 2711657 2717400 - 1 chr6 1817197 1824444 - 1 chr6 3251955 3257666 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4330227 4333845 1 1 chr10 2711657 2717400 1 2 chr6 1817197 1824444 1 3 chr6 3251955 3257666 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5181112 | 5185580 | a | 0 | + | | chr1 | 5181112 | 5185231 | a | 0 | + | | chr1 | 2940247 | 2947072 | a | 0 | - | | chr2 | 4005610 | 4009489 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 5181112 | 5188818 | a | 0 | + | | chr15 | 5181112 | 5184340 | a | 0 | + | | chrX | 8333031 | 8333033 | a | 0 | + | | chrY | 2 | 1349 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpabl21y3i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2940247 2947072 - 1 chr1 5181112 5185580 + 2 chr13 5181112 5188818 + 1 chr15 5181112 5184340 + 1 chr2 4005610 4009489 + 1 chr3 5181112 5187937 - 1 chr4 5181112 5184221 + 1 chr4 7529290 7536104 + 1 chrX 8333031 8333033 + 1 chrY 2 1349 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2940247 2947072 1 1 chr1 5181112 5185580 2 2 chr13 5181112 5188818 1 3 chr15 5181112 5184340 1 4 chr2 4005610 4009489 1 5 chr3 5181112 5187937 1 6 chr4 5181112 5184221 1 7 chr4 7529290 7536104 1 8 chrX 8333031 8333033 1 9 chrY 2 1349 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 8294643 | 8294645 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpiwzjhvuh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr4 8294643 8294645 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr4 8294643 8294645 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 9999999 | 10004610 | a | 0 | + | | chrX | 6327831 | 6337831 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpa9frmwvj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr9 9999999 10004610 + 1 chrX 6327831 6337831 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr9 9999999 10004610 1 1 chrX 6327831 6337831 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6221485 | 6225123 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpodnvnzi9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6221485 6225123 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6221485 6225123 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 6022063 | 6030621 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpl6o1gdy9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr15 6022063 6030621 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr15 6022063 6030621 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2795833 | 2796289 | a | 0 | + | | chr1 | 9480430 | 9485205 | a | 0 | + | | chr1 | 9070852 | 9080851 | a | 0 | + | | chr1 | 5287733 | 5290279 | a | 0 | + | | chr3 | 7981836 | 7985754 | a | 0 | + | | chr3 | 2383357 | 2388684 | a | 0 | - | | chr8 | 1668889 | 1672290 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmph38snyp_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2795833 2796289 + 1 chr1 5287733 5290279 + 1 chr1 9070852 9080851 + 1 chr1 9480430 9485205 + 1 chr3 2383357 2388684 - 1 chr3 7981836 7985754 + 1 chr8 1668889 1672290 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2795833 2796289 1 1 chr1 5287733 5290279 1 2 chr1 9070852 9080851 1 3 chr1 9480430 9485205 1 4 chr3 2383357 2388684 1 5 chr3 7981836 7985754 1 6 chr8 1668889 1672290 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6653511 | 6653512 | a | 0 | - | | chr1 | 3542915 | 3551272 | a | 0 | - | | chr2 | 1700406 | 1707083 | a | 0 | - | | chr15 | 2441590 | 2446456 | a | 0 | - | | chrM | 6645610 | 6646231 | a | 0 | + | | chrY | 7196713 | 7206084 | a | 0 | + | | chrY | 4074559 | 4080687 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpqyl_01qw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3542915 3551272 - 1 chr1 6653511 6653512 - 1 chr15 2441590 2446456 - 1 chr2 1700406 1707083 - 1 chrM 6645610 6646231 + 1 chrY 4074559 4080687 - 1 chrY 7196713 7206084 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3542915 3551272 1 1 chr1 6653511 6653512 1 2 chr15 2441590 2446456 1 3 chr2 1700406 1707083 1 4 chrM 6645610 6646231 1 5 chrY 4074559 4080687 1 6 chrY 7196713 7206084 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5739799 | 5743113 | a | 0 | + | | chr1 | 5063392 | 5069928 | a | 0 | + | | chr1 | 4433248 | 4433504 | a | 0 | + | | chr1 | 9999999 | 10007561 | a | 0 | - | | chr3 | 5644222 | 5649010 | a | 0 | - | | chr11 | 849434 | 858924 | a | 0 | - | | chrM | 3673282 | 3674238 | a | 0 | - | | chrY | 1844812 | 1846226 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpo_dg288_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4433248 4433504 + 1 chr1 5063392 5069928 + 1 chr1 5739799 5743113 + 1 chr1 9999999 10007561 - 1 chr11 849434 858924 - 1 chr3 5644222 5649010 - 1 chrM 3673282 3674238 - 1 chrY 1844812 1846226 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4433248 4433504 1 1 chr1 5063392 5069928 1 2 chr1 5739799 5743113 1 3 chr1 9999999 10007561 1 4 chr11 849434 858924 1 5 chr3 5644222 5649010 1 6 chrM 3673282 3674238 1 7 chrY 1844812 1846226 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8398770 | 8400086 | a | 0 | + | | chr1 | 4986915 | 4995751 | a | 0 | + | | chr1 | 1941975 | 1949097 | a | 0 | + | | chr1 | 2899965 | 2904976 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1941975 | 1949097 | a | 0 | + | | chr1 | 2899965 | 2904976 | a | 0 | + | | chr1 | 9350155 | 9357346 | a | 0 | + | | chr1 | 6458257 | 6465448 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpt1axarsk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1941975 1949097 + 1 chr1 2899965 2904976 + 1 chr1 4986915 4995751 + 1 chr1 6458257 6465448 - 1 chr1 8398770 8400086 + 1 chr1 9350155 9357346 + 1 chr19 7025275 7035274 + 1 chr20 5441424 5448615 + 1 chrX 306297 313488 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1941975 1949097 1 1 chr1 2899965 2904976 1 2 chr1 4986915 4995751 1 3 chr1 6458257 6465448 1 4 chr1 8398770 8400086 1 5 chr1 9350155 9357346 1 6 chr19 7025275 7035274 1 7 chr20 5441424 5448615 1 8 chrX 306297 313488 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr18 | 8997800 | 9001805 | a | 0 | + | | chr18 | 4550931 | 4555871 | a | 0 | + | | chr18 | 7690665 | 7690965 | a | 0 | + | | chr18 | 3710690 | 3715839 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr18 | 4951177 | 4960353 | a | 0 | + | | chr18 | 7420067 | 7425860 | a | 0 | + | | chr18 | 4609834 | 4612043 | a | 0 | + | | chr18 | 558137 | 561998 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmptpccxs0u/f1.bed) resultresultresultresultresultresultresultresultresultresult chr18 558137 561998 + 1 chr18 3710690 3715839 + 1 chr18 4550931 4555871 + 1 chr18 4609834 4612043 + 1 chr18 4951177 4960353 + 1 chr18 7420067 7425860 + 1 chr18 7448370 7450391 + 1 chr18 7690665 7690965 + 1 chr18 8979602 8982493 + 1 chr18 8997800 9001805 + 1 chr18 9004432 9005676 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr18 558137 561998 1 1 chr18 3710690 3715839 1 2 chr18 4550931 4555871 1 3 chr18 4609834 4612043 1 4 chr18 4951177 4960353 1 5 chr18 7420067 7425860 1 6 chr18 7448370 7450391 1 7 chr18 7690665 7690965 1 8 chr18 8979602 8982493 1 9 chr18 8997800 9001805 1 10 chr18 9004432 9005676 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr18 | 700506 | 708973 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpz10jkbbs/f1.bed) resultresultresultresultresultresultresultresultresultresult chr18 700506 708973 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr18 700506 708973 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6539016 | 6546101 | a | 0 | + | | chr1 | 5445874 | 5448177 | a | 0 | + | | chr1 | 4386443 | 4394761 | a | 0 | - | | chr5 | 3389277 | 3396362 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmphkdt2dtg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4386443 4394761 - 1 chr1 5445874 5448177 + 1 chr1 6539016 6546101 + 1 chr5 3389277 3396362 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4386443 4394761 1 1 chr1 5445874 5448177 1 2 chr1 6539016 6546101 1 3 chr5 3389277 3396362 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8664773 | 8665452 | a | 0 | + | | chr1 | 8674311 | 8681097 | a | 0 | - | | chr9 | 9418854 | 9420582 | a | 0 | - | | chr11 | 1640175 | 1646162 | a | 0 | + | | chr13 | 290845 | 292209 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_vdjasld/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8664773 8665452 + 1 chr1 8674311 8681097 - 1 chr11 1640175 1646162 + 1 chr13 290845 292209 - 1 chr9 9418854 9420582 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8664773 8665452 1 1 chr1 8674311 8681097 1 2 chr11 1640175 1646162 1 3 chr13 290845 292209 1 4 chr9 9418854 9420582 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3938085 | 3946383 | a | 0 | + | | chr1 | 2789578 | 2790474 | a | 0 | + | | chr1 | 9740903 | 9745970 | a | 0 | + | | chr5 | 5652051 | 5661337 | a | 0 | - | | chr7 | 3765355 | 3773048 | a | 0 | + | | chr20 | 7259658 | 7268944 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpcmss4kp2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2789578 2790474 + 1 chr1 3938085 3946383 + 1 chr1 9740903 9745970 + 1 chr20 7259658 7268944 - 1 chr5 5652051 5661337 - 1 chr7 3765355 3773048 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2789578 2790474 1 1 chr1 3938085 3946383 1 2 chr1 9740903 9745970 1 3 chr20 7259658 7268944 1 4 chr5 5652051 5661337 1 5 chr7 3765355 3773048 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2802667 | 2807557 | a | 0 | + | | chr1 | 3275845 | 3282507 | a | 0 | - | | chr1 | 8158921 | 8160114 | a | 0 | - | | chr1 | 1 | 7727 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr19 | 2144668 | 2151708 | a | 0 | - | | chr19 | 2591517 | 2596225 | a | 0 | - | | chr19 | 8158921 | 8167160 | a | 0 | - | | chr19 | 7587661 | 7589890 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpy9ox6yag/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7727 - 1 chr1 2802667 2807557 + 1 chr1 3275845 3282507 - 1 chr1 8158921 8160114 - 1 chr10 8158921 8168180 - 1 chr19 2144668 2151708 - 1 chr19 2591517 2596225 - 1 chr19 7587661 7589890 - 1 chr19 8158921 8167160 - 1 chr5 3440521 3446496 + 1 chr9 4492410 4494826 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 7727 1 1 chr1 2802667 2807557 1 2 chr1 3275845 3282507 1 3 chr1 8158921 8160114 1 4 chr10 8158921 8168180 1 5 chr19 2144668 2151708 1 6 chr19 2591517 2596225 1 7 chr19 7587661 7589890 1 8 chr19 8158921 8167160 1 9 chr5 3440521 3446496 1 10 chr9 4492410 4494826 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6020851 | 6025784 | a | 0 | + | | chr1 | 6020851 | 6027225 | a | 0 | + | | chr1 | 6020851 | 6024255 | a | 0 | + | | chr2 | 1412189 | 1417122 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 6020851 | 6030293 | a | 0 | + | | chr13 | 6020851 | 6028795 | a | 0 | + | | chr16 | 5355938 | 5360871 | a | 0 | + | | chrM | 9551264 | 9556197 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp6kkh8iir/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6020851 6027225 + 3 chr10 6020851 6025767 - 1 chr12 6020851 6030293 + 1 chr13 6020851 6028795 + 1 chr16 5355938 5360871 + 1 chr2 1412189 1417122 + 1 chr7 2067860 2076618 - 1 chr7 6020851 6025784 + 1 chrM 9551264 9556197 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6020851 6027225 3 1 chr10 6020851 6025767 1 2 chr12 6020851 6030293 1 3 chr13 6020851 6028795 1 4 chr16 5355938 5360871 1 5 chr2 1412189 1417122 1 6 chr7 2067860 2076618 1 7 chr7 6020851 6025784 1 8 chrM 9551264 9556197 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8091722 | 8097862 | a | 0 | + | | chr1 | 354825 | 362772 | a | 0 | + | | chr1 | 4185905 | 4191506 | a | 0 | - | | chr3 | 4896862 | 4897747 | a | 0 | + | | chr3 | 7638903 | 7643365 | a | 0 | + | | chr3 | 7026046 | 7035341 | a | 0 | - | | chr12 | 864526 | 866506 | a | 0 | + | | chr12 | 4313502 | 4315748 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp61mf_usw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 354825 362772 + 1 chr1 4185905 4191506 - 1 chr1 8091722 8097862 + 1 chr12 864526 866506 + 1 chr12 4313502 4315748 - 1 chr3 4896862 4897747 + 1 chr3 7026046 7035341 - 1 chr3 7638903 7643365 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 354825 362772 1 1 chr1 4185905 4191506 1 2 chr1 8091722 8097862 1 3 chr12 864526 866506 1 4 chr12 4313502 4315748 1 5 chr3 4896862 4897747 1 6 chr3 7026046 7035341 1 7 chr3 7638903 7643365 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr19 | 1007652 | 1008996 | a | 0 | - | | chrM | 5800991 | 5807423 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpv5l1dejq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr19 1007652 1008996 - 1 chrM 5800991 5807423 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr19 1007652 1008996 1 1 chrM 5800991 5807423 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4098161 | 4098162 | a | 0 | + | | chr1 | 4206200 | 4216199 | a | 0 | + | | chr1 | 3823421 | 3831472 | a | 0 | - | | chr5 | 6323280 | 6330493 | a | 0 | + | | chr8 | 2824462 | 2826108 | a | 0 | + | | chr19 | 7339228 | 7345937 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpcxjjoiap/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3823421 3831472 - 1 chr1 4098161 4098162 + 1 chr1 4206200 4216199 + 1 chr19 7339228 7345937 - 1 chr5 6323280 6330493 + 1 chr8 2824462 2826108 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3823421 3831472 1 1 chr1 4098161 4098162 1 2 chr1 4206200 4216199 1 3 chr19 7339228 7345937 1 4 chr5 6323280 6330493 1 5 chr8 2824462 2826108 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1633388 | 1638594 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpjco9im8c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1633388 1638594 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1633388 1638594 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1203808 | 1212202 | a | 0 | + | | chr6 | 1 | 2154 | a | 0 | + | | chr6 | 1972336 | 1981232 | a | 0 | + | | chr6 | 4696785 | 4704901 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpbl7begjk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1203808 1212202 + 1 chr6 1 2154 + 1 chr6 1972336 1981232 + 1 chr6 4696785 4704901 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1203808 1212202 1 1 chr6 1 2154 1 2 chr6 1972336 1981232 1 3 chr6 4696785 4704901 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2923549 | 2932545 | a | 0 | - | | chr1 | 9540828 | 9543313 | a | 0 | - | | chr1 | 8930486 | 8931856 | a | 0 | - | | chr2 | 8488452 | 8497236 | a | 0 | + | | chr15 | 6678756 | 6679755 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpywnit0kx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2923549 2932545 - 1 chr1 8930486 8931856 - 1 chr1 9540828 9543313 - 1 chr15 6678756 6679755 + 1 chr2 8488452 8497236 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2923549 2932545 1 1 chr1 8930486 8931856 1 2 chr1 9540828 9543313 1 3 chr15 6678756 6679755 1 4 chr2 8488452 8497236 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9351567 | 9353805 | a | 0 | - | | chr8 | 6188525 | 6191067 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_1z1t_ua/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9351567 9353805 - 1 chr8 6188525 6191067 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9351567 9353805 1 1 chr8 6188525 6191067 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7535833 | 7537391 | a | 0 | + | | chr1 | 9905032 | 9909339 | a | 0 | - | | chr20 | 3970951 | 3979286 | a | 0 | - | | chrM | 3249448 | 3254122 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpt_kz_zi1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7535833 7537391 + 1 chr1 9905032 9909339 - 1 chr20 3970951 3979286 - 1 chrM 3249448 3254122 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7535833 7537391 1 1 chr1 9905032 9909339 1 2 chr20 3970951 3979286 1 3 chrM 3249448 3254122 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4192433 | 4201891 | a | 0 | + | | chr1 | 6785449 | 6793219 | a | 0 | + | | chr1 | 4811157 | 4815561 | a | 0 | + | | chr1 | 671426 | 676879 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 9683296 | 9686522 | a | 0 | + | | chr18 | 10000000 | 10010000 | a | 0 | + | | chr18 | 10000000 | 10000063 | a | 0 | + | | chrY | 3294819 | 3302406 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpt7fhq_m9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 671426 676879 - 1 chr1 3069564 3075184 - 1 chr1 4192433 4201891 + 1 chr1 4811157 4815561 + 1 chr1 6650231 6657793 - 1 chr1 6785449 6793219 + 1 chr12 9683296 9686522 + 1 chr18 10000000 10010000 + 2 chr6 4907362 4911507 + 1 chrY 3294819 3302406 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 671426 676879 1 1 chr1 3069564 3075184 1 2 chr1 4192433 4201891 1 3 chr1 4811157 4815561 1 4 chr1 6650231 6657793 1 5 chr1 6785449 6793219 1 6 chr12 9683296 9686522 1 7 chr18 10000000 10010000 2 8 chr6 4907362 4911507 1 9 chrY 3294819 3302406 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 42514 | 42860 | a | 0 | + | | chr1 | 1 | 3487 | a | 0 | + | | chr1 | 9857225 | 9858115 | a | 0 | + | | chr1 | 8008544 | 8010606 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 8008544 | 8010606 | a | 0 | - | | chr1 | 2882594 | 2884234 | a | 0 | - | | chr1 | 5274373 | 5277790 | a | 0 | - | | chr1 | 5413841 | 5418393 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmptsk9o_69/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3487 + 1 chr1 42514 42860 + 1 chr1 2882594 2884234 - 1 chr1 5274373 5277790 - 1 chr1 5413841 5418393 - 1 chr1 8008544 8010606 - 1 chr1 9857225 9858115 + 1 chr21 7946795 7951650 - 1 chr8 84523 93124 - 1 chrM 9613003 9618538 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 3487 1 1 chr1 42514 42860 1 2 chr1 2882594 2884234 1 3 chr1 5274373 5277790 1 4 chr1 5413841 5418393 1 5 chr1 8008544 8010606 1 6 chr1 9857225 9858115 1 7 chr21 7946795 7951650 1 8 chr8 84523 93124 1 9 chrM 9613003 9618538 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 8805659 | 8808422 | a | 0 | + | | chr20 | 9902307 | 9905070 | a | 0 | + | | chr20 | 9667417 | 9674052 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpp01s_61q/f1.bed) resultresultresultresultresultresultresultresultresultresult chr2 8805659 8808422 + 1 chr20 9667417 9674052 + 1 chr20 9902307 9905070 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr2 8805659 8808422 1 1 chr20 9667417 9674052 1 2 chr20 9902307 9905070 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4747830 | 4749605 | a | 0 | + | | chr1 | 7049344 | 7051119 | a | 0 | + | | chr1 | 7604207 | 7605982 | a | 0 | + | | chr1 | 10000000 | 10001775 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7608546 | 7608547 | a | 0 | + | | chr1 | 3353910 | 3355685 | a | 0 | - | | chr1 | 7110609 | 7112384 | a | 0 | - | | chr1 | 4298986 | 4305037 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp11mrauoy/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3353910 3355685 - 1 chr1 4298986 4305037 - 1 chr1 4747830 4749605 + 1 chr1 7049344 7051119 + 1 chr1 7110609 7112384 - 1 chr1 7604207 7605982 + 1 chr1 7608546 7608547 + 1 chr1 9721201 9721492 + 1 chr1 10000000 10001775 + 1 chr14 9295855 9297630 + 1 chr15 6625675 6629993 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3353910 3355685 1 1 chr1 4298986 4305037 1 2 chr1 4747830 4749605 1 3 chr1 7049344 7051119 1 4 chr1 7110609 7112384 1 5 chr1 7604207 7605982 1 6 chr1 7608546 7608547 1 7 chr1 9721201 9721492 1 8 chr1 10000000 10001775 1 9 chr14 9295855 9297630 1 10 chr15 6625675 6629993 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 271161 | 274677 | a | 0 | + | | chr5 | 5560866 | 5566494 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp7cfn8zmk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 271161 274677 + 1 chr5 5560866 5566494 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 271161 274677 1 1 chr5 5560866 5566494 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9099123 | 9103078 | a | 0 | + | | chr1 | 2715254 | 2718757 | a | 0 | - | | chr1 | 5956025 | 5957046 | a | 0 | - | | chr6 | 8107692 | 8107892 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrX | 4492887 | 4497847 | a | 0 | + | | chrX | 2524270 | 2529650 | a | 0 | - | | chrX | 8107692 | 8116309 | a | 0 | - | | chrX | 651613 | 653235 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_itx7ok2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2715254 2718757 - 1 chr1 5956025 5957046 - 1 chr1 9099123 9103078 + 1 chr10 9999999 10004498 - 1 chr6 8107692 8107892 + 1 chrX 1 8276 + 1 chrX 651613 653235 - 1 chrX 2524270 2529650 - 1 chrX 4492887 4497847 + 1 chrX 8107692 8116309 - 1 chrX 10000000 10005957 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2715254 2718757 1 1 chr1 5956025 5957046 1 2 chr1 9099123 9103078 1 3 chr10 9999999 10004498 1 4 chr6 8107692 8107892 1 5 chrX 1 8276 1 6 chrX 651613 653235 1 7 chrX 2524270 2529650 1 8 chrX 4492887 4497847 1 9 chrX 8107692 8116309 1 10 chrX 10000000 10005957 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9734280 | 9741852 | a | 0 | + | | chr1 | 3933838 | 3941410 | a | 0 | - | | chr2 | 2355924 | 2363496 | a | 0 | - | | chr5 | 2249695 | 2257267 | a | 0 | + | | chr8 | 3358075 | 3365647 | a | 0 | + | | chr19 | 3829842 | 3837414 | a | 0 | - | | chrM | 7570174 | 7577746 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp217zi5ck/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3933838 3941410 - 1 chr1 9734280 9741852 + 1 chr19 3829842 3837414 - 1 chr2 2355924 2363496 - 1 chr5 2249695 2257267 + 1 chr8 3358075 3365647 + 1 chrM 7570174 7577746 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3933838 3941410 1 1 chr1 9734280 9741852 1 2 chr19 3829842 3837414 1 3 chr2 2355924 2363496 1 4 chr5 2249695 2257267 1 5 chr8 3358075 3365647 1 6 chrM 7570174 7577746 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3252663 | 3254244 | a | 0 | - | | chrX | 3846773 | 3855092 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpf8ggeybf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3252663 3254244 - 1 chrX 3846773 3855092 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3252663 3254244 1 1 chrX 3846773 3855092 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3198661 | 3198663 | a | 0 | + | | chr1 | 412936 | 418477 | a | 0 | + | | chr1 | 6604149 | 6610307 | a | 0 | + | | chr1 | 2065812 | 2075376 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 6344046 | 6345828 | a | 0 | + | | chr13 | 6472186 | 6472188 | a | 0 | - | | chr17 | 8160708 | 8164917 | a | 0 | - | | chr22 | 5821513 | 5829584 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3qzhglmh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 412936 418477 + 1 chr1 1865985 1870940 + 1 chr1 2065812 2075376 + 1 chr1 3198661 3200107 + 2 chr1 6141291 6148150 - 1 chr1 6604149 6610307 + 1 chr13 6344046 6345828 + 1 chr13 6472186 6472188 - 1 chr17 8160708 8164917 - 1 chr22 5821513 5829584 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 412936 418477 1 1 chr1 1865985 1870940 1 2 chr1 2065812 2075376 1 3 chr1 3198661 3200107 2 4 chr1 6141291 6148150 1 5 chr1 6604149 6610307 1 6 chr13 6344046 6345828 1 7 chr13 6472186 6472188 1 8 chr17 8160708 8164917 1 9 chr22 5821513 5829584 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6327979 | 6330734 | a | 0 | - | | chr1 | 1118850 | 1121605 | a | 0 | - | | chr1 | 828433 | 831188 | a | 0 | - | | chr4 | 1130425 | 1133180 | a | 0 | - | | chr5 | 3279582 | 3282337 | a | 0 | - | | chr11 | 634318 | 637073 | a | 0 | - | | chr19 | 3585941 | 3588696 | a | 0 | - | | chr19 | 7359553 | 7362308 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8_6ebdz_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 828433 831188 - 1 chr1 1118850 1121605 - 1 chr1 6327979 6330734 - 1 chr11 634318 637073 - 1 chr19 3585941 3588696 - 1 chr19 7359553 7362308 - 1 chr4 1130425 1133180 - 1 chr5 3279582 3282337 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 828433 831188 1 1 chr1 1118850 1121605 1 2 chr1 6327979 6330734 1 3 chr11 634318 637073 1 4 chr19 3585941 3588696 1 5 chr19 7359553 7362308 1 6 chr4 1130425 1133180 1 7 chr5 3279582 3282337 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 972122 | 975328 | a | 0 | + | | chr1 | 186676 | 194603 | a | 0 | + | | chr1 | 5032134 | 5038282 | a | 0 | - | | chr1 | 2 | 6636 | a | 0 | - | | chr1 | 5174218 | 5179637 | a | 0 | - | | chr7 | 1 | 8035 | a | 0 | + | | chr17 | 6303603 | 6306859 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpb1mwer6m/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 6636 - 1 chr1 186676 194603 + 1 chr1 972122 975328 + 1 chr1 5032134 5038282 - 1 chr1 5174218 5179637 - 1 chr17 6303603 6306859 + 1 chr7 1 8035 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2 6636 1 1 chr1 186676 194603 1 2 chr1 972122 975328 1 3 chr1 5032134 5038282 1 4 chr1 5174218 5179637 1 5 chr17 6303603 6306859 1 6 chr7 1 8035 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10001525 | a | 0 | - | | chr3 | 4297755 | 4299280 | a | 0 | + | | chr10 | 933069 | 941146 | a | 0 | + | | chr17 | 9590334 | 9598491 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_rtylq4x/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 10000000 10001525 - 1 chr10 933069 941146 + 1 chr17 9590334 9598491 - 1 chr3 4297755 4299280 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 10000000 10001525 1 1 chr10 933069 941146 1 2 chr17 9590334 9598491 1 3 chr3 4297755 4299280 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6762739 | 6767651 | a | 0 | + | | chr1 | 5012752 | 5017421 | a | 0 | - | | chr1 | 5789681 | 5794960 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmphqjsj1st/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5012752 5017421 - 1 chr1 5789681 5794960 - 1 chr1 6762739 6767651 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5012752 5017421 1 1 chr1 5789681 5794960 1 2 chr1 6762739 6767651 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1965451 | 1966888 | a | 0 | + | | chr1 | 8986293 | 8991340 | a | 0 | + | | chr1 | 588311 | 596806 | a | 0 | - | | chr1 | 2607361 | 2615495 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 7252237 | 7257284 | a | 0 | - | | chr12 | 8878814 | 8879470 | a | 0 | + | | chr20 | 1704694 | 1710862 | a | 0 | + | | chrX | 6488300 | 6490757 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpnqcsjpu7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 588311 596806 - 1 chr1 1435451 1437921 - 1 chr1 1965451 1966888 + 1 chr1 2607361 2615495 - 1 chr1 8986293 8991340 + 1 chr12 8878814 8879470 + 1 chr20 1704694 1710862 + 1 chr7 7252237 7257284 - 1 chrX 6488300 6490757 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 588311 596806 1 1 chr1 1435451 1437921 1 2 chr1 1965451 1966888 1 3 chr1 2607361 2615495 1 4 chr1 8986293 8991340 1 5 chr12 8878814 8879470 1 6 chr20 1704694 1710862 1 7 chr7 7252237 7257284 1 8 chrX 6488300 6490757 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 400197 | 408008 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpd0fdyflh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr6 400197 408008 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr6 400197 408008 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7904072 | 7904739 | a | 0 | - | | chr1 | 7587315 | 7587982 | a | 0 | - | | chr1 | 7504765 | 7509874 | a | 0 | - | | chr1 | 6830866 | 6840620 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 2701427 | 2702051 | a | 0 | - | | chr19 | 3334271 | 3334938 | a | 0 | + | | chr19 | 5026218 | 5036086 | a | 0 | - | | chr22 | 303281 | 304030 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1ri0u5hm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6830866 6840620 - 1 chr1 7504765 7509874 - 1 chr1 7587315 7587982 - 1 chr1 7904072 7904739 - 1 chr18 2701427 2702051 - 1 chr19 3334271 3334938 + 1 chr19 5026218 5036086 - 1 chr22 303281 304030 - 1 chr6 9122438 9123105 - 1 chr9 4785597 4791732 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6830866 6840620 1 1 chr1 7504765 7509874 1 2 chr1 7587315 7587982 1 3 chr1 7904072 7904739 1 4 chr18 2701427 2702051 1 5 chr19 3334271 3334938 1 6 chr19 5026218 5036086 1 7 chr22 303281 304030 1 8 chr6 9122438 9123105 1 9 chr9 4785597 4791732 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr20 | 7851763 | 7856637 | a | 0 | + | | chr20 | 2002885 | 2010928 | a | 0 | + | | chr20 | 9697480 | 9699175 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfy8kwm13/f1.bed) resultresultresultresultresultresultresultresultresultresult chr20 2002885 2010928 + 1 chr20 7851763 7856637 + 1 chr20 9697480 9699175 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr20 2002885 2010928 1 1 chr20 7851763 7856637 1 2 chr20 9697480 9699175 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4782383 | 4788734 | a | 0 | + | | chr1 | 3021474 | 3022781 | a | 0 | - | | chr1 | 1921097 | 1922404 | a | 0 | - | | chr14 | 9620329 | 9623716 | a | 0 | + | | chrX | 3381807 | 3383114 | a | 0 | + | | chrY | 7634304 | 7639778 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp5xpfv0qf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1921097 1922404 - 1 chr1 3021474 3022781 - 1 chr1 4782383 4788734 + 1 chr14 9620329 9623716 + 1 chrX 3381807 3383114 + 1 chrY 7634304 7639778 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1921097 1922404 1 1 chr1 3021474 3022781 1 2 chr1 4782383 4788734 1 3 chr14 9620329 9623716 1 4 chrX 3381807 3383114 1 5 chrY 7634304 7639778 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 1163040 | 1167320 | a | 0 | + | | chr14 | 4753175 | 4760459 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpc_6uw_6p/f1.bed) resultresultresultresultresultresultresultresultresultresult chr14 4753175 4760459 + 1 chr5 1163040 1167320 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr14 4753175 4760459 1 1 chr5 1163040 1167320 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7433998 | 7440073 | a | 0 | + | | chr1 | 6257596 | 6261733 | a | 0 | + | | chr1 | 6586335 | 6595958 | a | 0 | + | | chr2 | 6253652 | 6257789 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 7077903 | 7080459 | a | 0 | + | | chr16 | 1661932 | 1668035 | a | 0 | - | | chr18 | 8829912 | 8834205 | a | 0 | + | | chr21 | 9974737 | 9983949 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpbi034q4d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6257596 6261733 + 1 chr1 6586335 6595958 + 1 chr1 7433998 7440073 + 1 chr12 7077903 7080459 + 1 chr16 1661932 1668035 - 1 chr18 8829912 8834205 + 1 chr2 6253652 6257789 + 1 chr2 9036216 9040353 + 1 chr21 9974737 9983949 - 1 chr5 3574832 3583641 + 1 chr7 679377 683554 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6257596 6261733 1 1 chr1 6586335 6595958 1 2 chr1 7433998 7440073 1 3 chr12 7077903 7080459 1 4 chr16 1661932 1668035 1 5 chr18 8829912 8834205 1 6 chr2 6253652 6257789 1 7 chr2 9036216 9040353 1 8 chr21 9974737 9983949 1 9 chr5 3574832 3583641 1 10 chr7 679377 683554 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7244502 | 7244733 | a | 0 | - | | chr1 | 5396575 | 5402273 | a | 0 | - | | chr5 | 9140436 | 9142664 | a | 0 | + | | chr10 | 1767355 | 1770345 | a | 0 | + | | chr12 | 4651360 | 4656975 | a | 0 | + | | chrX | 1651339 | 1656992 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpeccj4crc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5396575 5402273 - 1 chr1 7244502 7244733 - 1 chr10 1767355 1770345 + 1 chr12 4651360 4656975 + 1 chr5 9140436 9142664 + 1 chrX 1651339 1656992 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5396575 5402273 1 1 chr1 7244502 7244733 1 2 chr10 1767355 1770345 1 3 chr12 4651360 4656975 1 4 chr5 9140436 9142664 1 5 chrX 1651339 1656992 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 641968 | 642769 | a | 0 | + | | chr1 | 641968 | 647125 | a | 0 | + | | chr1 | 641968 | 642220 | a | 0 | + | | chr1 | 641968 | 649577 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr17 | 641968 | 642273 | a | 0 | + | | chr18 | 6755196 | 6764079 | a | 0 | + | | chr20 | 511497 | 513600 | a | 0 | - | | chr21 | 5311979 | 5312397 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9eenc426/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 641968 649577 + 4 chr1 8142998 8146132 + 1 chr17 641968 642273 + 1 chr18 6755196 6764079 + 1 chr20 511497 513600 - 1 chr21 5311979 5312397 + 1 chr7 4095534 4095889 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 641968 649577 4 1 chr1 8142998 8146132 1 2 chr17 641968 642273 1 3 chr18 6755196 6764079 1 4 chr20 511497 513600 1 5 chr21 5311979 5312397 1 6 chr7 4095534 4095889 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7521859 | 7531053 | a | 0 | + | | chr1 | 6951468 | 6955192 | a | 0 | - | | chr12 | 6564083 | 6568055 | a | 0 | + | | chr12 | 7521859 | 7526441 | a | 0 | - | | chrM | 8111970 | 8120318 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpncqy0nb8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6951468 6955192 - 1 chr1 7521859 7531053 + 1 chr12 6564083 6568055 + 1 chr12 7521859 7526441 - 1 chrM 8111970 8120318 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6951468 6955192 1 1 chr1 7521859 7531053 1 2 chr12 6564083 6568055 1 3 chr12 7521859 7526441 1 4 chrM 8111970 8120318 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6355066 | 6364483 | a | 0 | + | | chr1 | 3339910 | 3342403 | a | 0 | + | | chr1 | 5679369 | 5679585 | a | 0 | - | | chr1 | 4926017 | 4933802 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 3339910 | 3343482 | a | 0 | + | | chr16 | 2876561 | 2883669 | a | 0 | + | | chr19 | 1159541 | 1162034 | a | 0 | + | | chrM | 8360447 | 8364031 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2dem39pr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3339910 3342403 + 2 chr1 4926017 4933802 - 1 chr1 5679369 5679585 - 1 chr1 6355066 6364483 + 1 chr1 7981220 7990714 - 1 chr10 4406432 4415140 - 1 chr14 3339910 3343482 + 1 chr16 2876561 2883669 + 1 chr19 1159541 1162034 + 1 chrM 8360447 8364031 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3339910 3342403 2 1 chr1 4926017 4933802 1 2 chr1 5679369 5679585 1 3 chr1 6355066 6364483 1 4 chr1 7981220 7990714 1 5 chr10 4406432 4415140 1 6 chr14 3339910 3343482 1 7 chr16 2876561 2883669 1 8 chr19 1159541 1162034 1 9 chrM 8360447 8364031 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8608634 | 8614661 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpkmru_rfa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8608634 8614661 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8608634 8614661 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3898650 | 3899951 | a | 0 | + | | chr1 | 2918482 | 2922539 | a | 0 | + | | chr1 | 2313637 | 2316646 | a | 0 | - | | chr1 | 7383136 | 7390317 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 3701804 | 3711803 | a | 0 | + | | chr17 | 3056479 | 3057277 | a | 0 | - | | chr21 | 10000000 | 10001377 | a | 0 | + | | chrM | 4511595 | 4517159 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpxpaw6uwe/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2313637 2316646 - 1 chr1 2918482 2922539 + 1 chr1 3898650 3899951 + 1 chr1 4969832 4972802 - 1 chr1 7383136 7390317 - 1 chr1 8981452 8982305 - 1 chr1 9833694 9833714 - 1 chr15 3701804 3711803 + 1 chr17 3056479 3057277 - 1 chr21 10000000 10001377 + 1 chrM 4511595 4517159 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2313637 2316646 1 1 chr1 2918482 2922539 1 2 chr1 3898650 3899951 1 3 chr1 4969832 4972802 1 4 chr1 7383136 7390317 1 5 chr1 8981452 8982305 1 6 chr1 9833694 9833714 1 7 chr15 3701804 3711803 1 8 chr17 3056479 3057277 1 9 chr21 10000000 10001377 1 10 chrM 4511595 4517159 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1020871 | 1024634 | a | 0 | + | | chr9 | 1894620 | 1901088 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpdefiyqti/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1020871 1024634 + 1 chr9 1894620 1901088 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1020871 1024634 1 1 chr9 1894620 1901088 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6863654 | 6870443 | a | 0 | + | | chr1 | 7089478 | 7094613 | a | 0 | - | | chr11 | 8135058 | 8143994 | a | 0 | + | | chr14 | 9648 | 14783 | a | 0 | + | | chr16 | 5736739 | 5736740 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpddrchs5f/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6863654 6870443 + 1 chr1 7089478 7094613 - 1 chr11 8135058 8143994 + 1 chr14 9648 14783 + 1 chr16 5736739 5736740 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6863654 6870443 1 1 chr1 7089478 7094613 1 2 chr11 8135058 8143994 1 3 chr14 9648 14783 1 4 chr16 5736739 5736740 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 7141830 | 7151830 | a | 0 | - | | chr19 | 177328 | 187328 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpizya_vfh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr19 177328 187328 - 1 chr6 7141830 7151830 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr19 177328 187328 1 1 chr6 7141830 7151830 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4887626 | 4887927 | a | 0 | + | | chr1 | 2666077 | 2674079 | a | 0 | - | | chr1 | 3282316 | 3291159 | a | 0 | - | | chr9 | 3282316 | 3282318 | a | 0 | - | | chr18 | 431503 | 440191 | a | 0 | + | | chr22 | 8959474 | 8968371 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpe7nxh5rg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2666077 2674079 - 1 chr1 3282316 3291159 - 1 chr1 4887626 4887927 + 1 chr18 431503 440191 + 1 chr22 8959474 8968371 + 1 chr9 3282316 3282318 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2666077 2674079 1 1 chr1 3282316 3291159 1 2 chr1 4887626 4887927 1 3 chr18 431503 440191 1 4 chr22 8959474 8968371 1 5 chr9 3282316 3282318 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6074250 | 6079511 | a | 0 | + | | chr1 | 222630 | 230767 | a | 0 | + | | chr1 | 67727 | 77438 | a | 0 | + | | chr1 | 2482083 | 2486010 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2482083 | 2486010 | a | 0 | + | | chr1 | 3947631 | 3957488 | a | 0 | + | | chr1 | 2482083 | 2487193 | a | 0 | - | | chr1 | 2482083 | 2486666 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpw6277nvt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 67727 77438 + 1 chr1 222630 230767 + 1 chr1 2482083 2487193 + 3 chr1 3947631 3957488 + 1 chr1 6074250 6079511 + 1 chr13 2482083 2485924 - 1 chr4 2482083 2489327 + 1 chr6 2482083 2482085 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 67727 77438 1 1 chr1 222630 230767 1 2 chr1 2482083 2487193 3 3 chr1 3947631 3957488 1 4 chr1 6074250 6079511 1 5 chr13 2482083 2485924 1 6 chr4 2482083 2489327 1 7 chr6 2482083 2482085 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2347854 | 2353283 | a | 0 | + | | chr1 | 7582913 | 7585648 | a | 0 | - | | chr1 | 2730334 | 2736817 | a | 0 | - | | chr4 | 2347854 | 2355314 | a | 0 | - | | chr5 | 2347854 | 2353665 | a | 0 | + | | chr5 | 7361417 | 7370555 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmplmdri4w1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2347854 2353283 + 1 chr1 2730334 2736817 - 1 chr1 7582913 7585648 - 1 chr4 2347854 2355314 - 1 chr5 2347854 2353665 + 1 chr5 7361417 7370555 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2347854 2353283 1 1 chr1 2730334 2736817 1 2 chr1 7582913 7585648 1 3 chr4 2347854 2355314 1 4 chr5 2347854 2353665 1 5 chr5 7361417 7370555 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 10000000 | 10003550 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp39a2tkr6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr2 10000000 10003550 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr2 10000000 10003550 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5574413 | 5581946 | a | 0 | + | | chr1 | 2499061 | 2506964 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpsirw3djx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2499061 2506964 - 1 chr1 5574413 5581946 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2499061 2506964 1 1 chr1 5574413 5581946 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9479493 | 9486904 | a | 0 | + | | chr1 | 336856 | 342101 | a | 0 | + | | chr1 | 9747788 | 9750392 | a | 0 | + | | chr1 | 9839928 | 9846535 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 5241273 | 5247136 | a | 0 | - | | chr17 | 4883884 | 4890562 | a | 0 | - | | chr22 | 7415602 | 7425254 | a | 0 | - | | chrY | 2 | 4734 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpau29obnk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 336856 342101 + 1 chr1 6114124 6119203 - 1 chr1 9479493 9486904 + 1 chr1 9747788 9750392 + 1 chr1 9839928 9846535 - 1 chr11 9654419 9655103 - 1 chr13 5241273 5247136 - 1 chr17 4883884 4890562 - 1 chr22 7415602 7425254 - 1 chr4 6942586 6947463 - 1 chrY 2 4734 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 336856 342101 1 1 chr1 6114124 6119203 1 2 chr1 9479493 9486904 1 3 chr1 9747788 9750392 1 4 chr1 9839928 9846535 1 5 chr11 9654419 9655103 1 6 chr13 5241273 5247136 1 7 chr17 4883884 4890562 1 8 chr22 7415602 7425254 1 9 chr4 6942586 6947463 1 10 chrY 2 4734 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1618367 | 1619229 | a | 0 | - | | chr1 | 1199915 | 1202573 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmppwiamljl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1199915 1202573 - 1 chr1 1618367 1619229 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1199915 1202573 1 1 chr1 1618367 1619229 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2839465 | 2840509 | a | 0 | + | | chrM | 6024288 | 6033839 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpnkbjinpt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2839465 2840509 + 1 chrM 6024288 6033839 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2839465 2840509 1 1 chrM 6024288 6033839 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 740718 | 749602 | a | 0 | + | | chr1 | 6998350 | 7007413 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1hi16cdk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 740718 749602 + 1 chr1 6998350 7007413 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 740718 749602 1 1 chr1 6998350 7007413 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr19 | 8930680 | 8932021 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp6winykt0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr19 8930680 8932021 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr19 8930680 8932021 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4980357 | 4982540 | a | 0 | + | | chrX | 5824574 | 5825677 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpij951s97/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4980357 4982540 + 1 chrX 5824574 5825677 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4980357 4982540 1 1 chrX 5824574 5825677 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2632687 | 2634748 | a | 0 | + | | chr1 | 8363074 | 8370913 | a | 0 | + | | chr1 | 6501016 | 6509789 | a | 0 | + | | chr1 | 4636990 | 4639202 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 2757870 | 2759036 | a | 0 | - | | chr7 | 3154852 | 3163627 | a | 0 | - | | chr10 | 7339489 | 7339786 | a | 0 | - | | chrX | 3431611 | 3436765 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2khn806d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1923993 1929671 - 1 chr1 2632687 2634748 + 1 chr1 3197422 3198031 - 1 chr1 4636990 4639202 + 1 chr1 6501016 6509789 + 1 chr1 8363074 8370913 + 1 chr1 9305491 9306657 - 1 chr10 7339489 7339786 - 1 chr3 2757870 2759036 - 1 chr7 3154852 3163627 - 1 chrX 3431611 3436765 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1923993 1929671 1 1 chr1 2632687 2634748 1 2 chr1 3197422 3198031 1 3 chr1 4636990 4639202 1 4 chr1 6501016 6509789 1 5 chr1 8363074 8370913 1 6 chr1 9305491 9306657 1 7 chr10 7339489 7339786 1 8 chr3 2757870 2759036 1 9 chr7 3154852 3163627 1 10 chrX 3431611 3436765 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1589122 | 1599122 | a | 0 | + | | chr1 | 2602042 | 2607712 | a | 0 | + | | chr1 | 7717441 | 7723111 | a | 0 | - | | chr1 | 6256499 | 6262169 | a | 0 | - | | chr11 | 2817813 | 2823483 | a | 0 | - | | chr19 | 2941713 | 2947889 | a | 0 | - | | chr20 | 1027908 | 1035699 | a | 0 | + | | chrM | 843379 | 849049 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpzoxawygf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1589122 1599122 + 1 chr1 2602042 2607712 + 1 chr1 6256499 6262169 - 1 chr1 7717441 7723111 - 1 chr11 2817813 2823483 - 1 chr19 2941713 2947889 - 1 chr20 1027908 1035699 + 1 chrM 843379 849049 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1589122 1599122 1 1 chr1 2602042 2607712 1 2 chr1 6256499 6262169 1 3 chr1 7717441 7723111 1 4 chr11 2817813 2823483 1 5 chr19 2941713 2947889 1 6 chr20 1027908 1035699 1 7 chrM 843379 849049 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9523455 | 9529134 | a | 0 | + | | chr1 | 9523455 | 9530940 | a | 0 | + | | chr4 | 9523455 | 9527510 | a | 0 | + | | chr13 | 3042943 | 3046998 | a | 0 | - | | chr14 | 4578010 | 4582065 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpq_h89asb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9523455 9530940 + 2 chr13 3042943 3046998 - 1 chr14 4578010 4582065 - 1 chr4 9523455 9527510 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9523455 9530940 2 1 chr13 3042943 3046998 1 2 chr14 4578010 4582065 1 3 chr4 9523455 9527510 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 389443 | 397818 | a | 0 | + | | chr8 | 664902 | 670627 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpiukr7to4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr7 389443 397818 + 1 chr8 664902 670627 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr7 389443 397818 1 1 chr8 664902 670627 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 599086 | 605654 | a | 0 | + | | chr1 | 8846306 | 8850615 | a | 0 | + | | chr1 | 616630 | 618524 | a | 0 | - | | chrX | 7456328 | 7462549 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpn4gx3mz3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 599086 605654 + 1 chr1 616630 618524 - 1 chr1 8846306 8850615 + 1 chrX 7456328 7462549 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 599086 605654 1 1 chr1 616630 618524 1 2 chr1 8846306 8850615 1 3 chrX 7456328 7462549 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6586122 | 6586904 | a | 0 | + | | chr1 | 8583723 | 8593644 | a | 0 | + | | chr1 | 7583565 | 7587983 | a | 0 | + | | chr1 | 8784094 | 8786190 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 1882759 | 1891050 | a | 0 | + | | chr17 | 3641143 | 3647678 | a | 0 | - | | chr18 | 2 | 495 | a | 0 | + | | chr20 | 10000000 | 10008433 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp0q2o05o9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3382899 3392899 - 1 chr1 6586122 6586904 + 1 chr1 7583565 7587983 + 1 chr1 8583723 8593644 + 1 chr1 8784094 8786190 - 1 chr10 4773634 4778311 + 1 chr12 1882759 1891050 + 1 chr17 3641143 3647678 - 1 chr18 2 495 + 1 chr20 10000000 10008433 + 1 chr8 8770610 8776232 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3382899 3392899 1 1 chr1 6586122 6586904 1 2 chr1 7583565 7587983 1 3 chr1 8583723 8593644 1 4 chr1 8784094 8786190 1 5 chr10 4773634 4778311 1 6 chr12 1882759 1891050 1 7 chr17 3641143 3647678 1 8 chr18 2 495 1 9 chr20 10000000 10008433 1 10 chr8 8770610 8776232 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2934223 | 2942594 | a | 0 | + | | chr1 | 2934223 | 2936269 | a | 0 | + | | chr1 | 522441 | 527140 | a | 0 | + | | chr1 | 2934223 | 2940031 | a | 0 | - | | chr1 | 2934223 | 2940919 | a | 0 | - | | chr13 | 2934223 | 2939029 | a | 0 | + | | chr13 | 5590376 | 5592675 | a | 0 | + | | chr13 | 2934223 | 2936522 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp457h24gl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 522441 527140 + 1 chr1 2934223 2942594 + 4 chr13 2934223 2939029 + 2 chr13 5590376 5592675 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 522441 527140 1 1 chr1 2934223 2942594 4 2 chr13 2934223 2939029 2 3 chr13 5590376 5592675 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 4108424 | 4110580 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpwrk0vshs/f1.bed) resultresultresultresultresultresultresultresultresultresult chr3 4108424 4110580 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr3 4108424 4110580 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4938338 | 4944591 | a | 0 | - | | chr14 | 6504025 | 6510775 | a | 0 | + | | chr14 | 8063292 | 8066999 | a | 0 | + | | chr14 | 5227750 | 5235321 | a | 0 | + | | chr14 | 5838990 | 5843795 | a | 0 | - | | chr14 | 10000000 | 10008218 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmprofff_fn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4938338 4944591 - 1 chr14 5227750 5235321 + 1 chr14 5838990 5843795 - 1 chr14 6504025 6510775 + 1 chr14 8063292 8066999 + 1 chr14 10000000 10008218 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4938338 4944591 1 1 chr14 5227750 5235321 1 2 chr14 5838990 5843795 1 3 chr14 6504025 6510775 1 4 chr14 8063292 8066999 1 5 chr14 10000000 10008218 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1439871 | 1442667 | a | 0 | + | | chr1 | 3841965 | 3841967 | a | 0 | + | | chr1 | 5297337 | 5300133 | a | 0 | + | | chr1 | 1 | 2797 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr15 | 6834124 | 6835377 | a | 0 | + | | chr20 | 9189540 | 9194246 | a | 0 | - | | chr22 | 4250379 | 4257232 | a | 0 | - | | chr22 | 9645472 | 9648268 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2hyoj5lr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2797 + 1 chr1 401541 404337 - 1 chr1 622933 626690 - 1 chr1 1439871 1442667 + 1 chr1 1648301 1651097 - 1 chr1 3841965 3841967 + 1 chr1 5297337 5300133 + 1 chr15 6834124 6835377 + 1 chr20 9189540 9194246 - 1 chr22 4250379 4257232 - 1 chr22 9645472 9648268 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2797 1 1 chr1 401541 404337 1 2 chr1 622933 626690 1 3 chr1 1439871 1442667 1 4 chr1 1648301 1651097 1 5 chr1 3841965 3841967 1 6 chr1 5297337 5300133 1 7 chr15 6834124 6835377 1 8 chr20 9189540 9194246 1 9 chr22 4250379 4257232 1 10 chr22 9645472 9648268 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9876097 | 9878460 | a | 0 | + | | chr1 | 7777097 | 7777123 | a | 0 | + | | chr1 | 2323210 | 2324660 | a | 0 | + | | chr1 | 9744758 | 9752748 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 104678 | 109170 | a | 0 | - | | chr14 | 1883435 | 1883461 | a | 0 | - | | chr20 | 740376 | 747467 | a | 0 | + | | chrM | 1 | 894 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpft7n1dv9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2323210 2324660 + 1 chr1 4099218 4107206 - 1 chr1 5841768 5846158 - 1 chr1 7777097 7777123 + 1 chr1 9744758 9752748 + 1 chr1 9876097 9878460 + 1 chr10 104678 109170 - 1 chr14 1883435 1883461 - 1 chr20 740376 747467 + 1 chr9 10000000 10004961 - 1 chrM 1 894 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2323210 2324660 1 1 chr1 4099218 4107206 1 2 chr1 5841768 5846158 1 3 chr1 7777097 7777123 1 4 chr1 9744758 9752748 1 5 chr1 9876097 9878460 1 6 chr10 104678 109170 1 7 chr14 1883435 1883461 1 8 chr20 740376 747467 1 9 chr9 10000000 10004961 1 10 chrM 1 894 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5370024 | 5374442 | a | 0 | + | | chr1 | 2133370 | 2137244 | a | 0 | - | | chr1 | 7945710 | 7950802 | a | 0 | - | | chr1 | 6643141 | 6646122 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 7945710 | 7955501 | a | 0 | - | | chr1 | 7410291 | 7411865 | a | 0 | - | | chr1 | 8138718 | 8147079 | a | 0 | - | | chr1 | 2711392 | 2721028 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp0ip11o4_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2133370 2137244 - 1 chr1 2711392 2721028 - 1 chr1 5370024 5374442 + 1 chr1 6643141 6646122 - 1 chr1 7410291 7411865 - 1 chr1 7945710 7955501 - 2 chr1 8138718 8147079 - 1 chr1 9508702 9512251 - 1 chr11 7945710 7952662 + 1 chr12 7945710 7950062 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2133370 2137244 1 1 chr1 2711392 2721028 1 2 chr1 5370024 5374442 1 3 chr1 6643141 6646122 1 4 chr1 7410291 7411865 1 5 chr1 7945710 7955501 2 6 chr1 8138718 8147079 1 7 chr1 9508702 9512251 1 8 chr11 7945710 7952662 1 9 chr12 7945710 7950062 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 284884 | 293568 | a | 0 | + | | chr1 | 3349364 | 3359314 | a | 0 | + | | chr1 | 3008519 | 3015979 | a | 0 | - | | chr1 | 2938430 | 2940133 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 1036052 | 1036790 | a | 0 | - | | chr19 | 3532337 | 3540321 | a | 0 | - | | chr21 | 460282 | 462860 | a | 0 | + | | chrY | 4958565 | 4961948 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8n3gxblp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 284884 293568 + 1 chr1 308252 313597 - 1 chr1 2938430 2940133 - 1 chr1 3008519 3015979 - 1 chr1 3349364 3359314 + 1 chr1 4541098 4549782 - 1 chr1 5772335 5779140 - 1 chr13 1036052 1036790 - 1 chr19 3532337 3540321 - 1 chr21 460282 462860 + 1 chrY 4958565 4961948 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 284884 293568 1 1 chr1 308252 313597 1 2 chr1 2938430 2940133 1 3 chr1 3008519 3015979 1 4 chr1 3349364 3359314 1 5 chr1 4541098 4549782 1 6 chr1 5772335 5779140 1 7 chr13 1036052 1036790 1 8 chr19 3532337 3540321 1 9 chr21 460282 462860 1 10 chrY 4958565 4961948 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8725323 | 8734541 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_5eqwsu2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8725323 8734541 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8725323 8734541 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7916412 | 7918464 | a | 0 | + | | chr2 | 4123408 | 4128623 | a | 0 | + | | chr2 | 6068284 | 6073877 | a | 0 | + | | chr2 | 5823348 | 5823747 | a | 0 | - | | chr10 | 9994908 | 10001612 | a | 0 | + | | chr19 | 9994908 | 10000783 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpf6spxuv9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7916412 7918464 + 1 chr10 9994908 10001612 + 1 chr19 9994908 10000783 - 1 chr2 4123408 4128623 + 1 chr2 5823348 5823747 - 1 chr2 6068284 6073877 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7916412 7918464 1 1 chr10 9994908 10001612 1 2 chr19 9994908 10000783 1 3 chr2 4123408 4128623 1 4 chr2 5823348 5823747 1 5 chr2 6068284 6073877 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 340341 | 347773 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpx8k5xxsz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr2 340341 347773 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr2 340341 347773 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 1157150 | 1166029 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpag0fb1xj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr7 1157150 1166029 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr7 1157150 1166029 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp06fnhug7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 __________ test_three_in_a_row[strandedness_chain433-method_chain433] __________ [gw3] linux -- Python 3.12.2 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_cluster[False] ______________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 strand = False @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:132: in test_cluster result = gr.cluster(strand=strand) pyranges/pyranges.py:1070: in cluster df = pyrange_apply_single(_cluster, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/cluster.py:14: in _cluster ids = annotate_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_cluster( E strand=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/annotate_clusters.pyx:15: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp6of9hb5d/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6584766 | 6592361 | a | 0 | + | | chr1 | 6131474 | 6132815 | a | 0 | + | | chr1 | 481429 | 485647 | a | 0 | + | | chr17 | 2894874 | 2903474 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpdx5o1h2b/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 481429 485647 a 0 + 1 1 chr1 6131474 6132815 a 0 + 2 2 chr1 6584766 6592361 a 0 + 3 3 chr17 2894874 2903474 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6584766 | 6592361 | a | 0 | + | | chr1 | 6131474 | 6132815 | a | 0 | + | | chr1 | 481429 | 485647 | a | 0 | + | | chr17 | 2894874 | 2903474 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6584766 | 6585089 | a | 0 | - | | chr1 | 2890015 | 2896308 | a | 0 | - | | chr2 | 6584766 | 6592409 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpkkm7gsel/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2890015 2896308 a 0 - 1 1 chr1 6584766 6585089 a 0 - 2 2 chr2 6584766 6592409 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6584766 | 6585089 | a | 0 | - | | chr1 | 2890015 | 2896308 | a | 0 | - | | chr2 | 6584766 | 6592409 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1901314 | 1902083 | a | 0 | + | | chr1 | 465045 | 465814 | a | 0 | + | | chr1 | 6584766 | 6585535 | a | 0 | - | | chr1 | 2894874 | 2895643 | a | 0 | - | | chr4 | 465045 | 465814 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmplqxrh07v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 465045 465814 a 0 + 1 1 chr1 1901314 1902083 a 0 + 2 2 chr1 2894874 2895643 a 0 - 3 3 chr1 6584766 6585535 a 0 - 4 4 chr4 465045 465814 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1901314 | 1902083 | a | 0 | + | | chr1 | 465045 | 465814 | a | 0 | + | | chr1 | 6584766 | 6585535 | a | 0 | - | | chr1 | 2894874 | 2895643 | a | 0 | - | | chr4 | 465045 | 465814 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1901314 | 1902083 | a | 0 | + | | chr1 | 465045 | 465814 | a | 0 | + | | chr1 | 6584766 | 6585535 | a | 0 | - | | chr1 | 2894874 | 2895643 | a | 0 | - | | chrY | 465045 | 465814 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmptxsbn5y_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 465045 465814 a 0 + 1 1 chr1 1901314 1902083 a 0 + 2 2 chr1 2894874 2895643 a 0 - 3 3 chr1 6584766 6585535 a 0 - 4 4 chrY 465045 465814 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1901314 | 1902083 | a | 0 | + | | chr1 | 465045 | 465814 | a | 0 | + | | chr1 | 6584766 | 6585535 | a | 0 | - | | chr1 | 2894874 | 2895643 | a | 0 | - | | chrY | 465045 | 465814 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6584766 | 6585535 | a | 0 | + | | chr1 | 1901314 | 1902083 | a | 0 | + | | chr1 | 465045 | 465814 | a | 0 | + | | chr1 | 2894874 | 2895643 | a | 0 | - | | chrY | 465045 | 465814 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpzi747lpa/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 465045 465814 a 0 + 1 1 chr1 1901314 1902083 a 0 + 2 2 chr1 2894874 2895643 a 0 - 3 3 chr1 6584766 6585535 a 0 + 4 4 chrY 465045 465814 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6584766 | 6585535 | a | 0 | + | | chr1 | 1901314 | 1902083 | a | 0 | + | | chr1 | 465045 | 465814 | a | 0 | + | | chr1 | 2894874 | 2895643 | a | 0 | - | | chrY | 465045 | 465814 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 459523 | 466210 | a | 0 | + | | chr1 | 196865 | 204293 | a | 0 | + | | chr1 | 459523 | 460548 | a | 0 | + | | chr1 | 459523 | 467204 | a | 0 | + | | chr1 | 459523 | 460548 | a | 0 | + | | chr1 | 459523 | 460292 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmplaa3_kh_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 196865 204293 a 0 + 1 1 chr1 459523 460292 a 0 - 2 2 chr1 459523 460548 a 0 + 2 3 chr1 459523 460548 a 0 + 2 4 chr1 459523 466210 a 0 + 2 5 chr1 459523 467204 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 459523 | 466210 | a | 0 | + | | chr1 | 196865 | 204293 | a | 0 | + | | chr1 | 459523 | 460548 | a | 0 | + | | chr1 | 459523 | 467204 | a | 0 | + | | chr1 | 459523 | 460548 | a | 0 | + | | chr1 | 459523 | 460292 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 770 | 1646 | a | 0 | + | | chr1 | 67332 | 68208 | a | 0 | + | | chr1 | 67332 | 68208 | a | 0 | + | | chr1 | 67332 | 68208 | a | 0 | - | | chr1 | 67332 | 68208 | a | 0 | - | | chr1 | 67332 | 73763 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpe69zi3f_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 770 1646 a 0 + 1 1 chr1 67332 68208 a 0 + 2 2 chr1 67332 68208 a 0 + 2 3 chr1 67332 68208 a 0 - 2 4 chr1 67332 68208 a 0 - 2 5 chr1 67332 73763 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 770 | 1646 | a | 0 | + | | chr1 | 67332 | 68208 | a | 0 | + | | chr1 | 67332 | 68208 | a | 0 | + | | chr1 | 67332 | 68208 | a | 0 | - | | chr1 | 67332 | 68208 | a | 0 | - | | chr1 | 67332 | 73763 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5433368 | 5434862 | a | 0 | - | | chr2 | 9689204 | 9698723 | a | 0 | - | | chr10 | 4759694 | 4768459 | a | 0 | + | | chrY | 8652696 | 8655058 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpkkagv02j/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5433368 5434862 a 0 - 1 1 chr10 4759694 4768459 a 0 + 2 2 chr2 9689204 9698723 a 0 - 3 3 chrY 8652696 8655058 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5433368 | 5434862 | a | 0 | - | | chr2 | 9689204 | 9698723 | a | 0 | - | | chr10 | 4759694 | 4768459 | a | 0 | + | | chrY | 8652696 | 8655058 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 149833 | 152653 | a | 0 | + | | chr1 | 149833 | 152653 | a | 0 | - | | chr2 | 149833 | 152653 | a | 0 | + | | chr10 | 149833 | 152653 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpgrjshmyk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 149833 152653 a 0 + 1 1 chr1 149833 152653 a 0 - 1 2 chr10 149833 152653 a 0 + 2 3 chr2 149833 152653 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 149833 | 152653 | a | 0 | + | | chr1 | 149833 | 152653 | a | 0 | - | | chr2 | 149833 | 152653 | a | 0 | + | | chr10 | 149833 | 152653 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpac65tfco/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpfvqcal8m/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_deyrsdb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpv3pr2cgs/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpzf91cmiv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmptk103ud2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1oaq1at0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp4aiks7hv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpjf7o7wwa/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpc9w0hcma/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpgh5pptgk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpsdocs0lb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 5964007 | 5968742 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp8q56cln4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr13 5964007 5968742 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 5964007 | 5968742 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9795733 | 9798241 | a | 0 | + | | chr1 | 7322947 | 7323890 | a | 0 | + | | chr1 | 4843315 | 4843404 | a | 0 | + | | chr1 | 1428291 | 1431759 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7861317 | 7870733 | a | 0 | + | | chr1 | 5126757 | 5127718 | a | 0 | + | | chr1 | 4904852 | 4908807 | a | 0 | + | | chr1 | 8723839 | 8731796 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpzfwk808r/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1428291 1431759 a 0 + 1 1 chr1 4843315 4843404 a 0 + 2 2 chr1 4904852 4908807 a 0 + 3 3 chr1 5126757 5127718 a 0 + 4 4 chr1 7322947 7323890 a 0 + 5 5 chr1 7861317 7870733 a 0 + 6 6 chr1 8723839 8731796 a 0 + 7 7 chr1 9795733 9798241 a 0 + 8 8 chr10 5187839 5191581 a 0 + 9 9 chr14 10000000 10003972 a 0 + 10 10 chr9 2304722 2311684 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9795733 | 9798241 | a | 0 | + | | chr1 | 7322947 | 7323890 | a | 0 | + | | chr1 | 4843315 | 4843404 | a | 0 | + | | chr1 | 1428291 | 1431759 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7861317 | 7870733 | a | 0 | + | | chr1 | 5126757 | 5127718 | a | 0 | + | | chr1 | 4904852 | 4908807 | a | 0 | + | | chr1 | 8723839 | 8731796 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 9400910 | 9406220 | a | 0 | - | | chr8 | 9400910 | 9409600 | a | 0 | - | | chr10 | 9400910 | 9403953 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbpcurd4b/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr10 9400910 9403953 a 0 + 1 1 chr4 9400910 9406220 a 0 - 2 2 chr8 9400910 9409600 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 9400910 | 9406220 | a | 0 | - | | chr8 | 9400910 | 9409600 | a | 0 | - | | chr10 | 9400910 | 9403953 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9895373 | 9901992 | a | 0 | + | | chr1 | 8406619 | 8412997 | a | 0 | + | | chr1 | 6969161 | 6978514 | a | 0 | + | | chr1 | 8406619 | 8408401 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 1 | 4902 | a | 0 | + | | chr15 | 2 | 8118 | a | 0 | + | | chr17 | 3256660 | 3262990 | a | 0 | + | | chr19 | 8406619 | 8411197 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp32pgxmre/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1149098 1155611 a 0 + 1 1 chr1 6540024 6546309 a 0 - 2 2 chr1 6969161 6978514 a 0 + 3 3 chr1 8406619 8408401 a 0 + 4 4 chr1 8406619 8412997 a 0 + 4 5 chr1 9028127 9028879 a 0 + 5 6 chr1 9895373 9901992 a 0 + 6 7 chr15 2 8118 a 0 + 7 8 chr17 3256660 3262990 a 0 + 8 9 chr19 8406619 8411197 a 0 + 9 10 chr2 1 4902 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9895373 | 9901992 | a | 0 | + | | chr1 | 8406619 | 8412997 | a | 0 | + | | chr1 | 6969161 | 6978514 | a | 0 | + | | chr1 | 8406619 | 8408401 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 1 | 4902 | a | 0 | + | | chr15 | 2 | 8118 | a | 0 | + | | chr17 | 3256660 | 3262990 | a | 0 | + | | chr19 | 8406619 | 8411197 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 15233 | 24771 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmph248jzn1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chrY 15233 24771 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 15233 | 24771 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 6623090 | 6633089 | a | 0 | + | | chr14 | 7434401 | 7438855 | a | 0 | - | | chr21 | 5515772 | 5516569 | a | 0 | + | | chr21 | 132006 | 137369 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr21 | 4523000 | 4527615 | a | 0 | + | | chr21 | 2271388 | 2272549 | a | 0 | + | | chr21 | 6634674 | 6644630 | a | 0 | - | | chr21 | 8452702 | 8458919 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp8m0_4q7j/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr13 6623090 6633089 a 0 + 1 1 chr14 7434401 7438855 a 0 - 2 2 chr21 132006 137369 a 0 + 3 3 chr21 2271388 2272549 a 0 + 4 4 chr21 4523000 4527615 a 0 + 5 5 chr21 5515772 5516569 a 0 + 6 6 chr21 5930688 5938496 a 0 + 7 7 chr21 6634674 6644630 a 0 - 8 8 chr21 8452702 8458919 a 0 - 9 9 chr21 8709056 8716274 a 0 + 10 10 chr21 8947438 8956397 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 6623090 | 6633089 | a | 0 | + | | chr14 | 7434401 | 7438855 | a | 0 | - | | chr21 | 5515772 | 5516569 | a | 0 | + | | chr21 | 132006 | 137369 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr21 | 4523000 | 4527615 | a | 0 | + | | chr21 | 2271388 | 2272549 | a | 0 | + | | chr21 | 6634674 | 6644630 | a | 0 | - | | chr21 | 8452702 | 8458919 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10008606 | a | 0 | + | | chr1 | 3193815 | 3202422 | a | 0 | + | | chr4 | 9625139 | 9633746 | a | 0 | - | | chr22 | 151682 | 160289 | a | 0 | + | | chrM | 9126942 | 9134203 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp56b1lfyd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3193815 3202422 a 0 + 1 1 chr1 9999999 10008606 a 0 + 2 2 chr22 151682 160289 a 0 + 3 3 chr4 9625139 9633746 a 0 - 4 4 chrM 9126942 9134203 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10008606 | a | 0 | + | | chr1 | 3193815 | 3202422 | a | 0 | + | | chr4 | 9625139 | 9633746 | a | 0 | - | | chr22 | 151682 | 160289 | a | 0 | + | | chrM | 9126942 | 9134203 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8979656 | 8981314 | a | 0 | + | | chr5 | 5964244 | 5968745 | a | 0 | - | | chr13 | 5432244 | 5433902 | a | 0 | + | | chr13 | 8979656 | 8981314 | a | 0 | + | | chr13 | 4493488 | 4495146 | a | 0 | - | | chrX | 7301507 | 7303165 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2esel6jp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8979656 8981314 a 0 + 1 1 chr13 4493488 4495146 a 0 - 2 2 chr13 5432244 5433902 a 0 + 3 3 chr13 8979656 8981314 a 0 + 4 4 chr5 5964244 5968745 a 0 - 5 5 chrX 7301507 7303165 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8979656 | 8981314 | a | 0 | + | | chr5 | 5964244 | 5968745 | a | 0 | - | | chr13 | 5432244 | 5433902 | a | 0 | + | | chr13 | 8979656 | 8981314 | a | 0 | + | | chr13 | 4493488 | 4495146 | a | 0 | - | | chrX | 7301507 | 7303165 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5982907 | 5983431 | a | 0 | + | | chr1 | 505480 | 508623 | a | 0 | + | | chr1 | 7213635 | 7219948 | a | 0 | + | | chr1 | 3853737 | 3861227 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr21 | 8719790 | 8729208 | a | 0 | + | | chr21 | 5404864 | 5412345 | a | 0 | + | | chrM | 3840029 | 3843081 | a | 0 | - | | chrM | 834922 | 841158 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp4ng6qpbz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 505480 508623 a 0 + 1 1 chr1 3853737 3861227 a 0 + 2 2 chr1 5982907 5983431 a 0 + 3 3 chr1 7066542 7072784 a 0 - 4 4 chr1 7213635 7219948 a 0 + 5 5 chr11 2927095 2931324 a 0 + 6 6 chr19 9917564 9920948 a 0 + 7 7 chr21 5404864 5412345 a 0 + 8 8 chr21 8719790 8729208 a 0 + 9 9 chrM 834922 841158 a 0 - 10 10 chrM 3840029 3843081 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5982907 | 5983431 | a | 0 | + | | chr1 | 505480 | 508623 | a | 0 | + | | chr1 | 7213635 | 7219948 | a | 0 | + | | chr1 | 3853737 | 3861227 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr21 | 8719790 | 8729208 | a | 0 | + | | chr21 | 5404864 | 5412345 | a | 0 | + | | chrM | 3840029 | 3843081 | a | 0 | - | | chrM | 834922 | 841158 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2310728 | 2318707 | a | 0 | - | | chr1 | 3182346 | 3189627 | a | 0 | - | | chr1 | 2310728 | 2316673 | a | 0 | - | | chr1 | 7791986 | 7799261 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 2310728 | 2317907 | a | 0 | - | | chr13 | 5307926 | 5316532 | a | 0 | - | | chr22 | 10000000 | 10004829 | a | 0 | - | | chrY | 7809403 | 7812365 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0s0yrqbh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2310728 2316673 a 0 - 1 1 chr1 2310728 2318707 a 0 - 1 2 chr1 3182346 3189627 a 0 - 2 3 chr1 7791986 7799261 a 0 - 3 4 chr13 2310728 2317907 a 0 - 4 5 chr13 5307926 5316532 a 0 - 5 6 chr22 10000000 10004829 a 0 - 6 7 chr4 2310728 2316789 a 0 - 7 8 chr5 2310728 2317002 a 0 - 8 9 chrY 2 8607 a 0 - 9 10 chrY 7809403 7812365 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2310728 | 2318707 | a | 0 | - | | chr1 | 3182346 | 3189627 | a | 0 | - | | chr1 | 2310728 | 2316673 | a | 0 | - | | chr1 | 7791986 | 7799261 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 2310728 | 2317907 | a | 0 | - | | chr13 | 5307926 | 5316532 | a | 0 | - | | chr22 | 10000000 | 10004829 | a | 0 | - | | chrY | 7809403 | 7812365 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2841685 | 2849322 | a | 0 | + | | chr1 | 2841685 | 2847390 | a | 0 | + | | chr1 | 4447780 | 4450245 | a | 0 | + | | chr1 | 2841685 | 2847176 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 2841685 | 2842318 | a | 0 | - | | chr6 | 2841685 | 2851039 | a | 0 | - | | chr11 | 5111819 | 5116151 | a | 0 | - | | chr19 | 2841685 | 2845863 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpsxyei8oo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2841685 2842586 a 0 - 1 1 chr1 2841685 2847176 a 0 - 1 2 chr1 2841685 2847390 a 0 + 1 3 chr1 2841685 2848812 a 0 - 1 4 chr1 2841685 2849093 a 0 - 1 5 chr1 2841685 2849322 a 0 + 1 6 chr1 4447780 4450245 a 0 + 2 7 chr11 5111819 5116151 a 0 - 3 8 chr19 2841685 2845863 a 0 - 4 9 chr5 2841685 2842318 a 0 - 5 10 chr6 2841685 2851039 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2841685 | 2849322 | a | 0 | + | | chr1 | 2841685 | 2847390 | a | 0 | + | | chr1 | 4447780 | 4450245 | a | 0 | + | | chr1 | 2841685 | 2847176 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 2841685 | 2842318 | a | 0 | - | | chr6 | 2841685 | 2851039 | a | 0 | - | | chr11 | 5111819 | 5116151 | a | 0 | - | | chr19 | 2841685 | 2845863 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5331552 | 5332530 | a | 0 | + | | chr1 | 3312079 | 3318467 | a | 0 | - | | chr4 | 8083620 | 8092615 | a | 0 | + | | chr13 | 3312079 | 3320892 | a | 0 | + | | chr14 | 3312079 | 3321294 | a | 0 | + | | chr15 | 3312079 | 3320391 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1bdmk2o6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3312079 3318467 a 0 - 1 1 chr1 5331552 5332530 a 0 + 2 2 chr13 3312079 3320892 a 0 + 3 3 chr14 3312079 3321294 a 0 + 4 4 chr15 3312079 3320391 a 0 + 5 5 chr4 8083620 8092615 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5331552 | 5332530 | a | 0 | + | | chr1 | 3312079 | 3318467 | a | 0 | - | | chr4 | 8083620 | 8092615 | a | 0 | + | | chr13 | 3312079 | 3320892 | a | 0 | + | | chr14 | 3312079 | 3321294 | a | 0 | + | | chr15 | 3312079 | 3320391 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5196049 | 5202028 | a | 0 | - | | chr1 | 5869874 | 5875853 | a | 0 | - | | chr1 | 5869874 | 5875853 | a | 0 | - | | chr1 | 3015457 | 3021436 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 5869874 | 5875853 | a | 0 | - | | chr13 | 8711453 | 8717432 | a | 0 | - | | chr21 | 9506953 | 9512932 | a | 0 | + | | chr22 | 5869874 | 5875853 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpvhhfvd0t/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2615334 2621313 a 0 - 1 1 chr1 3015457 3021436 a 0 - 2 2 chr1 5196049 5202028 a 0 - 3 3 chr1 5869874 5875853 a 0 - 4 4 chr1 5869874 5875853 a 0 - 4 5 chr13 5869874 5875853 a 0 - 5 6 chr13 8711453 8717432 a 0 - 6 7 chr21 9506953 9512932 a 0 + 7 8 chr22 5869874 5875853 a 0 - 8 9 chr8 5869874 5875853 a 0 - 9 10 chrM 5869874 5875853 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5196049 | 5202028 | a | 0 | - | | chr1 | 5869874 | 5875853 | a | 0 | - | | chr1 | 5869874 | 5875853 | a | 0 | - | | chr1 | 3015457 | 3021436 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 5869874 | 5875853 | a | 0 | - | | chr13 | 8711453 | 8717432 | a | 0 | - | | chr21 | 9506953 | 9512932 | a | 0 | + | | chr22 | 5869874 | 5875853 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1728481 | 1729869 | a | 0 | + | | chr1 | 1391435 | 1397276 | a | 0 | + | | chr1 | 8435966 | 8440104 | a | 0 | + | | chr1 | 10000000 | 10005667 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 557885 | 562169 | a | 0 | + | | chr1 | 3946602 | 3946879 | a | 0 | - | | chr1 | 7988480 | 7998319 | a | 0 | - | | chr1 | 1069841 | 1074252 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpf38xuq_8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 557885 562169 a 0 + 1 1 chr1 1069841 1074252 a 0 - 2 2 chr1 1391435 1397276 a 0 + 3 3 chr1 1728481 1729869 a 0 + 4 4 chr1 3946602 3946879 a 0 - 5 5 chr1 7988480 7998319 a 0 - 6 6 chr1 8435966 8440104 a 0 + 7 7 chr1 9454678 9456066 a 0 + 8 8 chr1 10000000 10005667 a 0 + 9 9 chr21 2058866 2065298 a 0 - 10 10 chrX 6830797 6832185 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1728481 | 1729869 | a | 0 | + | | chr1 | 1391435 | 1397276 | a | 0 | + | | chr1 | 8435966 | 8440104 | a | 0 | + | | chr1 | 10000000 | 10005667 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 557885 | 562169 | a | 0 | + | | chr1 | 3946602 | 3946879 | a | 0 | - | | chr1 | 7988480 | 7998319 | a | 0 | - | | chr1 | 1069841 | 1074252 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9729407 | 9735160 | a | 0 | + | | chr1 | 9729407 | 9735160 | a | 0 | - | | chr15 | 9729407 | 9735160 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmps33cu7ci/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9729407 9735160 a 0 + 1 1 chr1 9729407 9735160 a 0 - 1 2 chr15 9729407 9735160 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9729407 | 9735160 | a | 0 | + | | chr1 | 9729407 | 9735160 | a | 0 | - | | chr15 | 9729407 | 9735160 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7175877 | 7179119 | a | 0 | + | | chr1 | 7175877 | 7183993 | a | 0 | + | | chr1 | 7175877 | 7183282 | a | 0 | - | | chr5 | 7175877 | 7178388 | a | 0 | + | | chr13 | 7175877 | 7184896 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpp1w7eea_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7175877 7179119 a 0 + 1 1 chr1 7175877 7183282 a 0 - 1 2 chr1 7175877 7183993 a 0 + 1 3 chr13 7175877 7184896 a 0 - 2 4 chr5 7175877 7178388 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7175877 | 7179119 | a | 0 | + | | chr1 | 7175877 | 7183993 | a | 0 | + | | chr1 | 7175877 | 7183282 | a | 0 | - | | chr5 | 7175877 | 7178388 | a | 0 | + | | chr13 | 7175877 | 7184896 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 832210 | 836377 | a | 0 | + | | chr1 | 8554851 | 8555197 | a | 0 | + | | chr1 | 7755901 | 7756139 | a | 0 | - | | chr1 | 9690469 | 9694902 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 630298 | 638842 | a | 0 | + | | chr14 | 1570627 | 1572377 | a | 0 | - | | chr16 | 6487851 | 6489253 | a | 0 | + | | chr17 | 5691733 | 5697164 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7mth88uz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 832210 836377 a 0 + 1 1 chr1 7755901 7756139 a 0 - 2 2 chr1 8554851 8555197 a 0 + 3 3 chr1 9690469 9694902 a 0 - 4 4 chr14 630298 638842 a 0 + 5 5 chr14 1570627 1572377 a 0 - 6 6 chr16 6487851 6489253 a 0 + 7 7 chr17 5691733 5697164 a 0 - 8 8 chr21 2173967 2174831 a 0 - 9 9 chr4 3642315 3644709 a 0 + 10 10 chr4 4749835 4759573 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 832210 | 836377 | a | 0 | + | | chr1 | 8554851 | 8555197 | a | 0 | + | | chr1 | 7755901 | 7756139 | a | 0 | - | | chr1 | 9690469 | 9694902 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 630298 | 638842 | a | 0 | + | | chr14 | 1570627 | 1572377 | a | 0 | - | | chr16 | 6487851 | 6489253 | a | 0 | + | | chr17 | 5691733 | 5697164 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6694601 | 6700681 | a | 0 | + | | chr10 | 7073059 | 7082992 | a | 0 | + | | chr10 | 6694601 | 6703864 | a | 0 | + | | chr10 | 6694601 | 6702862 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 7581672 | 7582999 | a | 0 | - | | chr10 | 6694601 | 6695730 | a | 0 | - | | chr10 | 6694601 | 6696766 | a | 0 | - | | chr10 | 9159408 | 9161187 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpe1g0omby/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr10 6694601 6695730 a 0 - 1 1 chr10 6694601 6696766 a 0 - 1 2 chr10 6694601 6697927 a 0 + 1 3 chr10 6694601 6697970 a 0 + 1 4 chr10 6694601 6700681 a 0 + 1 5 chr10 6694601 6702862 a 0 + 1 6 chr10 6694601 6703864 a 0 + 1 7 chr10 7073059 7082992 a 0 + 2 8 chr10 7581672 7582999 a 0 - 3 9 chr10 8722379 8722868 a 0 + 4 10 chr10 9159408 9161187 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6694601 | 6700681 | a | 0 | + | | chr10 | 7073059 | 7082992 | a | 0 | + | | chr10 | 6694601 | 6703864 | a | 0 | + | | chr10 | 6694601 | 6702862 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 7581672 | 7582999 | a | 0 | - | | chr10 | 6694601 | 6695730 | a | 0 | - | | chr10 | 6694601 | 6696766 | a | 0 | - | | chr10 | 9159408 | 9161187 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4378986 | 4384674 | a | 0 | - | | chr1 | 7723020 | 7726089 | a | 0 | - | | chr1 | 5448874 | 5449179 | a | 0 | - | | chr1 | 5244494 | 5249633 | a | 0 | - | | chr7 | 4313638 | 4323637 | a | 0 | - | | chr10 | 6265253 | 6267553 | a | 0 | - | | chr15 | 2 | 9599 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpg5ekyvfn/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4378986 4384674 a 0 - 1 1 chr1 5244494 5249633 a 0 - 2 2 chr1 5448874 5449179 a 0 - 3 3 chr1 7723020 7726089 a 0 - 4 4 chr10 6265253 6267553 a 0 - 5 5 chr15 2 9599 a 0 - 6 6 chr7 4313638 4323637 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4378986 | 4384674 | a | 0 | - | | chr1 | 7723020 | 7726089 | a | 0 | - | | chr1 | 5448874 | 5449179 | a | 0 | - | | chr1 | 5244494 | 5249633 | a | 0 | - | | chr7 | 4313638 | 4323637 | a | 0 | - | | chr10 | 6265253 | 6267553 | a | 0 | - | | chr15 | 2 | 9599 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 2307754 | 2309034 | a | 0 | + | | chr9 | 9266997 | 9268277 | a | 0 | + | | chr19 | 958267 | 959547 | a | 0 | + | | chr21 | 5646801 | 5648081 | a | 0 | - | | chr21 | 42789 | 44069 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpyfiixu81/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr19 958267 959547 a 0 + 1 1 chr2 2307754 2309034 a 0 + 2 2 chr21 42789 44069 a 0 - 3 3 chr21 5646801 5648081 a 0 - 4 4 chr9 9266997 9268277 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 2307754 | 2309034 | a | 0 | + | | chr9 | 9266997 | 9268277 | a | 0 | + | | chr19 | 958267 | 959547 | a | 0 | + | | chr21 | 5646801 | 5648081 | a | 0 | - | | chr21 | 42789 | 44069 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6350490 | 6358554 | a | 0 | + | | chr1 | 6350490 | 6358554 | a | 0 | + | | chr1 | 6350490 | 6358554 | a | 0 | - | | chr1 | 6350490 | 6351888 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 1785710 | 1794171 | a | 0 | + | | chr15 | 6350490 | 6358554 | a | 0 | - | | chr18 | 6350490 | 6357198 | a | 0 | + | | chr22 | 6350490 | 6358554 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2sw2l1ev/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6350490 6351888 a 0 - 1 1 chr1 6350490 6358554 a 0 + 1 2 chr1 6350490 6358554 a 0 + 1 3 chr1 6350490 6358554 a 0 - 1 4 chr1 6350490 6358554 a 0 - 1 5 chr1 9134772 9142836 a 0 - 2 6 chr13 1785710 1794171 a 0 + 3 7 chr15 6350490 6358554 a 0 - 4 8 chr18 6350490 6357198 a 0 + 5 9 chr22 6350490 6358554 a 0 + 6 10 chr5 6350490 6358834 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6350490 | 6358554 | a | 0 | + | | chr1 | 6350490 | 6358554 | a | 0 | + | | chr1 | 6350490 | 6358554 | a | 0 | - | | chr1 | 6350490 | 6351888 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 1785710 | 1794171 | a | 0 | + | | chr15 | 6350490 | 6358554 | a | 0 | - | | chr18 | 6350490 | 6357198 | a | 0 | + | | chr22 | 6350490 | 6358554 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8521569 | 8528878 | a | 0 | + | | chr1 | 2727060 | 2730315 | a | 0 | + | | chr1 | 4047219 | 4057218 | a | 0 | - | | chr1 | 6699312 | 6701644 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 8521569 | 8527757 | a | 0 | + | | chr8 | 7364307 | 7368962 | a | 0 | - | | chr14 | 8521569 | 8524975 | a | 0 | - | | chrY | 8521569 | 8521570 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpnrffbzqp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1979405 1988363 a 0 - 1 1 chr1 2727060 2730315 a 0 + 2 2 chr1 4047219 4057218 a 0 - 3 3 chr1 6699312 6701644 a 0 - 4 4 chr1 8521569 8528878 a 0 + 5 5 chr14 8521569 8524975 a 0 - 6 6 chr4 2461573 2469766 a 0 + 7 7 chr5 8521569 8527757 a 0 + 8 8 chr8 7364307 7368962 a 0 - 9 9 chrY 8521569 8521570 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8521569 | 8528878 | a | 0 | + | | chr1 | 2727060 | 2730315 | a | 0 | + | | chr1 | 4047219 | 4057218 | a | 0 | - | | chr1 | 6699312 | 6701644 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 8521569 | 8527757 | a | 0 | + | | chr8 | 7364307 | 7368962 | a | 0 | - | | chr14 | 8521569 | 8524975 | a | 0 | - | | chrY | 8521569 | 8521570 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6745719 | 6754357 | a | 0 | - | | chr1 | 8848589 | 8851034 | a | 0 | - | | chr1 | 7599131 | 7607769 | a | 0 | - | | chr1 | 7556459 | 7562387 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 5620522 | 5625802 | a | 0 | + | | chr12 | 3186505 | 3187859 | a | 0 | + | | chr12 | 1503927 | 1512565 | a | 0 | - | | chr12 | 7485596 | 7495548 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpuxfwdy_w/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6745719 6754357 a 0 - 1 1 chr1 7556459 7562387 a 0 - 2 2 chr1 7599131 7607769 a 0 - 3 3 chr1 8848589 8851034 a 0 - 4 4 chr12 1503927 1512565 a 0 - 5 5 chr12 3186505 3187859 a 0 + 6 6 chr12 5620522 5625802 a 0 + 7 7 chr12 7485596 7495548 a 0 - 8 8 chr21 1 1274 a 0 - 9 9 chr4 9406231 9407142 a 0 - 10 10 chrX 9711996 9720710 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6745719 | 6754357 | a | 0 | - | | chr1 | 8848589 | 8851034 | a | 0 | - | | chr1 | 7599131 | 7607769 | a | 0 | - | | chr1 | 7556459 | 7562387 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 5620522 | 5625802 | a | 0 | + | | chr12 | 3186505 | 3187859 | a | 0 | + | | chr12 | 1503927 | 1512565 | a | 0 | - | | chr12 | 7485596 | 7495548 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3421240 | 3424167 | a | 0 | + | | chr1 | 2323971 | 2328896 | a | 0 | - | | chr1 | 1632570 | 1637495 | a | 0 | - | | chr1 | 2253321 | 2258246 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 4023481 | 4028406 | a | 0 | - | | chr14 | 2553649 | 2558574 | a | 0 | + | | chr19 | 9567997 | 9571041 | a | 0 | - | | chr21 | 5170839 | 5175764 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpr3e5r1va/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1632570 1637495 a 0 - 1 1 chr1 2253321 2258246 a 0 - 2 2 chr1 2323971 2328896 a 0 - 3 3 chr1 2391637 2394738 a 0 - 4 4 chr1 3421240 3424167 a 0 + 5 5 chr14 2553649 2558574 a 0 + 6 6 chr19 9567997 9571041 a 0 - 7 7 chr21 5170839 5175764 a 0 - 8 8 chr7 8143821 8148746 a 0 - 9 9 chr9 4023481 4028406 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3421240 | 3424167 | a | 0 | + | | chr1 | 2323971 | 2328896 | a | 0 | - | | chr1 | 1632570 | 1637495 | a | 0 | - | | chr1 | 2253321 | 2258246 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 4023481 | 4028406 | a | 0 | - | | chr14 | 2553649 | 2558574 | a | 0 | + | | chr19 | 9567997 | 9571041 | a | 0 | - | | chr21 | 5170839 | 5175764 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 5968501 | 5973965 | a | 0 | + | | chr18 | 9655624 | 9663951 | a | 0 | + | | chrM | 11691 | 14255 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpu__husby/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr11 5968501 5973965 a 0 + 1 1 chr18 9655624 9663951 a 0 + 2 2 chrM 11691 14255 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 5968501 | 5973965 | a | 0 | + | | chr18 | 9655624 | 9663951 | a | 0 | + | | chrM | 11691 | 14255 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 766910 | 776192 | a | 0 | - | | chr1 | 6409345 | 6417417 | a | 0 | - | | chr1 | 5116040 | 5121575 | a | 0 | - | | chr5 | 957602 | 965178 | a | 0 | + | | chr7 | 1 | 3119 | a | 0 | - | | chr13 | 3394198 | 3395046 | a | 0 | + | | chr16 | 2434722 | 2443686 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpn7u3cpr6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 766910 776192 a 0 - 1 1 chr1 5116040 5121575 a 0 - 2 2 chr1 6409345 6417417 a 0 - 3 3 chr13 3394198 3395046 a 0 + 4 4 chr16 2434722 2443686 a 0 - 5 5 chr5 957602 965178 a 0 + 6 6 chr7 1 3119 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 766910 | 776192 | a | 0 | - | | chr1 | 6409345 | 6417417 | a | 0 | - | | chr1 | 5116040 | 5121575 | a | 0 | - | | chr5 | 957602 | 965178 | a | 0 | + | | chr7 | 1 | 3119 | a | 0 | - | | chr13 | 3394198 | 3395046 | a | 0 | + | | chr16 | 2434722 | 2443686 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4778411 | 4785148 | a | 0 | - | | chr1 | 9606528 | 9609156 | a | 0 | - | | chr1 | 7049406 | 7051273 | a | 0 | - | | chr1 | 4071203 | 4076738 | a | 0 | - | | chr1 | 2960354 | 2969080 | a | 0 | - | | chr17 | 5082664 | 5084531 | a | 0 | - | | chr17 | 9844575 | 9852579 | a | 0 | - | | chr19 | 1848486 | 1852967 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpsaomjwop/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2960354 2969080 a 0 - 1 1 chr1 4071203 4076738 a 0 - 2 2 chr1 4778411 4785148 a 0 - 3 3 chr1 7049406 7051273 a 0 - 4 4 chr1 9606528 9609156 a 0 - 5 5 chr17 5082664 5084531 a 0 - 6 6 chr17 9844575 9852579 a 0 - 7 7 chr19 1848486 1852967 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4778411 | 4785148 | a | 0 | - | | chr1 | 9606528 | 9609156 | a | 0 | - | | chr1 | 7049406 | 7051273 | a | 0 | - | | chr1 | 4071203 | 4076738 | a | 0 | - | | chr1 | 2960354 | 2969080 | a | 0 | - | | chr17 | 5082664 | 5084531 | a | 0 | - | | chr17 | 9844575 | 9852579 | a | 0 | - | | chr19 | 1848486 | 1852967 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1476613 | 1484581 | a | 0 | + | | chr1 | 4180129 | 4183408 | a | 0 | + | | chr1 | 2246027 | 2252959 | a | 0 | + | | chr1 | 8618956 | 8624849 | a | 0 | - | | chr1 | 6547724 | 6551375 | a | 0 | - | | chr20 | 10000000 | 10002471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0413_e04/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1476613 1484581 a 0 + 1 1 chr1 2246027 2252959 a 0 + 2 2 chr1 4180129 4183408 a 0 + 3 3 chr1 6547724 6551375 a 0 - 4 4 chr1 8618956 8624849 a 0 - 5 5 chr20 10000000 10002471 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1476613 | 1484581 | a | 0 | + | | chr1 | 4180129 | 4183408 | a | 0 | + | | chr1 | 2246027 | 2252959 | a | 0 | + | | chr1 | 8618956 | 8624849 | a | 0 | - | | chr1 | 6547724 | 6551375 | a | 0 | - | | chr20 | 10000000 | 10002471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 336634 | 338293 | a | 0 | + | | chr1 | 6773726 | 6775967 | a | 0 | + | | chr1 | 8465083 | 8468555 | a | 0 | + | | chr1 | 5444989 | 5447230 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr17 | 9294108 | 9296349 | a | 0 | + | | chr19 | 8392324 | 8394565 | a | 0 | - | | chr20 | 2143382 | 2153271 | a | 0 | - | | chr22 | 9770447 | 9772688 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpg_g227ib/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 336634 338293 a 0 + 1 1 chr1 5444989 5447230 a 0 - 2 2 chr1 6773726 6775967 a 0 + 3 3 chr1 8465083 8468555 a 0 + 4 4 chr10 9999999 10006668 a 0 + 5 5 chr17 9294108 9296349 a 0 + 6 6 chr19 8392324 8394565 a 0 - 7 7 chr20 2143382 2153271 a 0 - 8 8 chr22 9770447 9772688 a 0 + 9 9 chr4 6563910 6566151 a 0 - 10 10 chr6 7157594 7159835 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 336634 | 338293 | a | 0 | + | | chr1 | 6773726 | 6775967 | a | 0 | + | | chr1 | 8465083 | 8468555 | a | 0 | + | | chr1 | 5444989 | 5447230 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr17 | 9294108 | 9296349 | a | 0 | + | | chr19 | 8392324 | 8394565 | a | 0 | - | | chr20 | 2143382 | 2153271 | a | 0 | - | | chr22 | 9770447 | 9772688 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3659025 | 3662681 | a | 0 | + | | chr1 | 10000000 | 10008687 | a | 0 | + | | chr1 | 7362717 | 7366892 | a | 0 | + | | chr1 | 268160 | 275467 | a | 0 | + | | chr1 | 2592740 | 2598505 | a | 0 | + | | chr21 | 6030797 | 6037511 | a | 0 | - | | chrX | 9179783 | 9187313 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpf63zb5_n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 268160 275467 a 0 + 1 1 chr1 2592740 2598505 a 0 + 2 2 chr1 3659025 3662681 a 0 + 3 3 chr1 7362717 7366892 a 0 + 4 4 chr1 10000000 10008687 a 0 + 5 5 chr21 6030797 6037511 a 0 - 6 6 chrX 9179783 9187313 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3659025 | 3662681 | a | 0 | + | | chr1 | 10000000 | 10008687 | a | 0 | + | | chr1 | 7362717 | 7366892 | a | 0 | + | | chr1 | 268160 | 275467 | a | 0 | + | | chr1 | 2592740 | 2598505 | a | 0 | + | | chr21 | 6030797 | 6037511 | a | 0 | - | | chrX | 9179783 | 9187313 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7080120 | 7085522 | a | 0 | + | | chr1 | 2962921 | 2972624 | a | 0 | + | | chr8 | 4425404 | 4435364 | a | 0 | + | | chr15 | 2883109 | 2891484 | a | 0 | + | | chr15 | 1579806 | 1585251 | a | 0 | + | | chrM | 2556424 | 2565167 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpgmznpeks/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2962921 2972624 a 0 + 1 1 chr1 7080120 7085522 a 0 + 2 2 chr15 1579806 1585251 a 0 + 3 3 chr15 2883109 2891484 a 0 + 4 4 chr8 4425404 4435364 a 0 + 5 5 chrM 2556424 2565167 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7080120 | 7085522 | a | 0 | + | | chr1 | 2962921 | 2972624 | a | 0 | + | | chr8 | 4425404 | 4435364 | a | 0 | + | | chr15 | 2883109 | 2891484 | a | 0 | + | | chr15 | 1579806 | 1585251 | a | 0 | + | | chrM | 2556424 | 2565167 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1968074 | 1972630 | a | 0 | + | | chr1 | 1190402 | 1196541 | a | 0 | - | | chr13 | 1968074 | 1968192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpxetoi7ga/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1190402 1196541 a 0 - 1 1 chr1 1968074 1972630 a 0 + 2 2 chr13 1968074 1968192 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1968074 | 1972630 | a | 0 | + | | chr1 | 1190402 | 1196541 | a | 0 | - | | chr13 | 1968074 | 1968192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2750201 | 2752422 | a | 0 | + | | chr1 | 468731 | 470952 | a | 0 | + | | chr7 | 2595819 | 2597357 | a | 0 | - | | chr16 | 10000000 | 10001155 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpey5k8vic/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 468731 470952 a 0 + 1 1 chr1 2750201 2752422 a 0 + 2 2 chr16 10000000 10001155 a 0 + 3 3 chr7 2595819 2597357 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2750201 | 2752422 | a | 0 | + | | chr1 | 468731 | 470952 | a | 0 | + | | chr7 | 2595819 | 2597357 | a | 0 | - | | chr16 | 10000000 | 10001155 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7620491 | 7625068 | a | 0 | + | | chr1 | 4879050 | 4883627 | a | 0 | + | | chr1 | 4435043 | 4439620 | a | 0 | - | | chr1 | 923797 | 923882 | a | 0 | - | | chr2 | 3741667 | 3744976 | a | 0 | + | | chr12 | 2250531 | 2255108 | a | 0 | - | | chr22 | 4427049 | 4431626 | a | 0 | + | | chrY | 1635240 | 1639817 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpjwtotbvy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 923797 923882 a 0 - 1 1 chr1 4435043 4439620 a 0 - 2 2 chr1 4879050 4883627 a 0 + 3 3 chr1 7620491 7625068 a 0 + 4 4 chr12 2250531 2255108 a 0 - 5 5 chr2 3741667 3744976 a 0 + 6 6 chr22 4427049 4431626 a 0 + 7 7 chrY 1635240 1639817 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7620491 | 7625068 | a | 0 | + | | chr1 | 4879050 | 4883627 | a | 0 | + | | chr1 | 4435043 | 4439620 | a | 0 | - | | chr1 | 923797 | 923882 | a | 0 | - | | chr2 | 3741667 | 3744976 | a | 0 | + | | chr12 | 2250531 | 2255108 | a | 0 | - | | chr22 | 4427049 | 4431626 | a | 0 | + | | chrY | 1635240 | 1639817 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8407724 | 8410892 | a | 0 | + | | chr1 | 7673814 | 7683482 | a | 0 | - | | chr1 | 8376011 | 8378215 | a | 0 | - | | chr5 | 8274655 | 8282876 | a | 0 | + | | chr5 | 944707 | 953626 | a | 0 | + | | chr11 | 407675 | 410773 | a | 0 | + | | chr20 | 5399899 | 5402998 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2oue9h19/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7673814 7683482 a 0 - 1 1 chr1 8376011 8378215 a 0 - 2 2 chr1 8407724 8410892 a 0 + 3 3 chr11 407675 410773 a 0 + 4 4 chr20 5399899 5402998 a 0 - 5 5 chr5 944707 953626 a 0 + 6 6 chr5 8274655 8282876 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8407724 | 8410892 | a | 0 | + | | chr1 | 7673814 | 7683482 | a | 0 | - | | chr1 | 8376011 | 8378215 | a | 0 | - | | chr5 | 8274655 | 8282876 | a | 0 | + | | chr5 | 944707 | 953626 | a | 0 | + | | chr11 | 407675 | 410773 | a | 0 | + | | chr20 | 5399899 | 5402998 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3803454 | 3807459 | a | 0 | + | | chr1 | 5858636 | 5862814 | a | 0 | + | | chr9 | 9199165 | 9203980 | a | 0 | + | | chr21 | 10000000 | 10008718 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpk7z34m9b/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3803454 3807459 a 0 + 1 1 chr1 5858636 5862814 a 0 + 2 2 chr21 10000000 10008718 a 0 + 3 3 chr9 9199165 9203980 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3803454 | 3807459 | a | 0 | + | | chr1 | 5858636 | 5862814 | a | 0 | + | | chr9 | 9199165 | 9203980 | a | 0 | + | | chr21 | 10000000 | 10008718 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4311042 | 4311044 | a | 0 | + | | chr1 | 4311042 | 4316126 | a | 0 | + | | chr1 | 4311042 | 4319786 | a | 0 | - | | chr1 | 4311042 | 4319776 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 4311042 | 4317046 | a | 0 | - | | chr8 | 4311042 | 4313147 | a | 0 | - | | chr14 | 4311042 | 4316428 | a | 0 | - | | chrX | 4311042 | 4316016 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmph_2ygyq4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1762728 1769961 a 0 - 1 1 chr1 4311042 4311044 a 0 + 2 2 chr1 4311042 4313147 a 0 - 2 3 chr1 4311042 4316126 a 0 + 2 4 chr1 4311042 4319776 a 0 - 2 5 chr1 4311042 4319786 a 0 - 2 6 chr14 4311042 4316428 a 0 - 3 7 chr5 4311042 4319965 a 0 + 4 8 chr7 4311042 4317046 a 0 - 5 9 chr8 4311042 4313147 a 0 - 6 10 chrX 4311042 4316016 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4311042 | 4311044 | a | 0 | + | | chr1 | 4311042 | 4316126 | a | 0 | + | | chr1 | 4311042 | 4319786 | a | 0 | - | | chr1 | 4311042 | 4319776 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 4311042 | 4317046 | a | 0 | - | | chr8 | 4311042 | 4313147 | a | 0 | - | | chr14 | 4311042 | 4316428 | a | 0 | - | | chrX | 4311042 | 4316016 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 2350360 | 2358089 | a | 0 | - | | chr17 | 3963021 | 3964332 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpj_61zhbq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr14 2350360 2358089 a 0 - 1 1 chr17 3963021 3964332 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 2350360 | 2358089 | a | 0 | - | | chr17 | 3963021 | 3964332 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2767340 | 2768552 | a | 0 | + | | chr1 | 9850787 | 9851999 | a | 0 | + | | chr9 | 4508255 | 4510376 | a | 0 | + | | chr11 | 9850787 | 9860787 | a | 0 | - | | chr11 | 9850787 | 9860787 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp8p6_kc57/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2767340 2768552 a 0 + 1 1 chr1 9850787 9851999 a 0 + 2 2 chr11 9850787 9860787 a 0 - 3 3 chr11 9850787 9860787 a 0 - 3 4 chr9 4508255 4510376 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2767340 | 2768552 | a | 0 | + | | chr1 | 9850787 | 9851999 | a | 0 | + | | chr9 | 4508255 | 4510376 | a | 0 | + | | chr11 | 9850787 | 9860787 | a | 0 | - | | chr11 | 9850787 | 9860787 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 7873591 | 7881581 | a | 0 | + | | chr6 | 3340970 | 3342295 | a | 0 | + | | chr6 | 2315995 | 2323640 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp917w32aq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr6 2315995 2323640 a 0 - 1 1 chr6 3340970 3342295 a 0 + 2 2 chr6 7873591 7881581 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 7873591 | 7881581 | a | 0 | + | | chr6 | 3340970 | 3342295 | a | 0 | + | | chr6 | 2315995 | 2323640 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4984821 | 4993642 | a | 0 | + | | chr1 | 3158268 | 3160055 | a | 0 | + | | chr1 | 420195 | 427954 | a | 0 | + | | chr1 | 9034320 | 9043162 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 4987526 | 4987527 | a | 0 | + | | chr18 | 7013805 | 7014630 | a | 0 | - | | chr22 | 4567766 | 4576145 | a | 0 | - | | chrX | 6620621 | 6628541 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp885blznp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 420195 427954 a 0 + 1 1 chr1 3158268 3160055 a 0 + 2 2 chr1 4984821 4993642 a 0 + 3 3 chr1 6620621 6627105 a 0 - 4 4 chr1 9034320 9043162 a 0 + 5 5 chr16 4987526 4987527 a 0 + 6 6 chr18 7013805 7014630 a 0 - 7 7 chr22 4567766 4576145 a 0 - 8 8 chr3 6620621 6630621 a 0 - 9 9 chr7 7659849 7668677 a 0 - 10 10 chrX 6620621 6628541 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4984821 | 4993642 | a | 0 | + | | chr1 | 3158268 | 3160055 | a | 0 | + | | chr1 | 420195 | 427954 | a | 0 | + | | chr1 | 9034320 | 9043162 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 4987526 | 4987527 | a | 0 | + | | chr18 | 7013805 | 7014630 | a | 0 | - | | chr22 | 4567766 | 4576145 | a | 0 | - | | chrX | 6620621 | 6628541 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9657749 | 9667212 | a | 0 | + | | chr1 | 3646054 | 3648333 | a | 0 | + | | chr1 | 5479747 | 5484227 | a | 0 | + | | chr1 | 3880700 | 3885180 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 9912063 | 9915741 | a | 0 | - | | chr7 | 7894920 | 7899400 | a | 0 | - | | chr16 | 9948500 | 9949310 | a | 0 | - | | chrM | 4680962 | 4684733 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpdzowhm6s/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3646054 3648333 a 0 + 1 1 chr1 3880700 3885180 a 0 - 2 2 chr1 5479747 5484227 a 0 + 3 3 chr1 7504293 7505253 a 0 - 4 4 chr1 8634019 8638499 a 0 - 5 5 chr1 9657749 9667212 a 0 + 6 6 chr16 9948500 9949310 a 0 - 7 7 chr4 7894920 7899400 a 0 + 8 8 chr5 9912063 9915741 a 0 - 9 9 chr7 7894920 7899400 a 0 - 10 10 chrM 4680962 4684733 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9657749 | 9667212 | a | 0 | + | | chr1 | 3646054 | 3648333 | a | 0 | + | | chr1 | 5479747 | 5484227 | a | 0 | + | | chr1 | 3880700 | 3885180 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 9912063 | 9915741 | a | 0 | - | | chr7 | 7894920 | 7899400 | a | 0 | - | | chr16 | 9948500 | 9949310 | a | 0 | - | | chrM | 4680962 | 4684733 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3224842 | 3234266 | a | 0 | + | | chr1 | 9490611 | 9500611 | a | 0 | - | | chr14 | 2 | 4636 | a | 0 | - | | chr21 | 2996151 | 2999413 | a | 0 | + | | chr21 | 6886125 | 6895159 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp48h01qfy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3224842 3234266 a 0 + 1 1 chr1 9490611 9500611 a 0 - 2 2 chr14 2 4636 a 0 - 3 3 chr21 2996151 2999413 a 0 + 4 4 chr21 6886125 6895159 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3224842 | 3234266 | a | 0 | + | | chr1 | 9490611 | 9500611 | a | 0 | - | | chr14 | 2 | 4636 | a | 0 | - | | chr21 | 2996151 | 2999413 | a | 0 | + | | chr21 | 6886125 | 6895159 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6183081 | 6184490 | a | 0 | + | | chr1 | 94720 | 104517 | a | 0 | - | | chr5 | 2711005 | 2717002 | a | 0 | + | | chr11 | 6829503 | 6833545 | a | 0 | + | | chr12 | 2453896 | 2455219 | a | 0 | + | | chr21 | 8070713 | 8070715 | a | 0 | - | | chr22 | 1052674 | 1062471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpf40dc7rq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 94720 104517 a 0 - 1 1 chr1 6183081 6184490 a 0 + 2 2 chr11 6829503 6833545 a 0 + 3 3 chr12 2453896 2455219 a 0 + 4 4 chr21 8070713 8070715 a 0 - 5 5 chr22 1052674 1062471 a 0 - 6 6 chr5 2711005 2717002 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6183081 | 6184490 | a | 0 | + | | chr1 | 94720 | 104517 | a | 0 | - | | chr5 | 2711005 | 2717002 | a | 0 | + | | chr11 | 6829503 | 6833545 | a | 0 | + | | chr12 | 2453896 | 2455219 | a | 0 | + | | chr21 | 8070713 | 8070715 | a | 0 | - | | chr22 | 1052674 | 1062471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4985116 | 4989805 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7i7ji7va/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4985116 4989805 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4985116 | 4989805 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7327632 | 7331871 | a | 0 | + | | chr1 | 4619138 | 4624695 | a | 0 | + | | chr1 | 1127092 | 1131096 | a | 0 | + | | chr1 | 6058870 | 6062292 | a | 0 | - | | chr1 | 10000000 | 10005413 | a | 0 | - | | chr1 | 9757133 | 9764080 | a | 0 | - | | chr1 | 3577378 | 3578873 | a | 0 | - | | chrM | 5229841 | 5233756 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpxzknvv49/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1127092 1131096 a 0 + 1 1 chr1 3577378 3578873 a 0 - 2 2 chr1 4619138 4624695 a 0 + 3 3 chr1 6058870 6062292 a 0 - 4 4 chr1 7327632 7331871 a 0 + 5 5 chr1 9757133 9764080 a 0 - 6 6 chr1 10000000 10005413 a 0 - 7 7 chrM 5229841 5233756 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7327632 | 7331871 | a | 0 | + | | chr1 | 4619138 | 4624695 | a | 0 | + | | chr1 | 1127092 | 1131096 | a | 0 | + | | chr1 | 6058870 | 6062292 | a | 0 | - | | chr1 | 10000000 | 10005413 | a | 0 | - | | chr1 | 9757133 | 9764080 | a | 0 | - | | chr1 | 3577378 | 3578873 | a | 0 | - | | chrM | 5229841 | 5233756 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1037818 | 1046797 | a | 0 | + | | chr1 | 4648965 | 4651695 | a | 0 | + | | chr2 | 6559235 | 6564156 | a | 0 | - | | chr3 | 45619 | 54107 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 8956947 | 8957425 | a | 0 | + | | chr17 | 1575075 | 1580662 | a | 0 | - | | chr21 | 849656 | 857251 | a | 0 | + | | chr22 | 638017 | 640415 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpsrsdcgr8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1037818 1046797 a 0 + 1 1 chr1 4648965 4651695 a 0 + 2 2 chr11 1059325 1060212 a 0 - 3 3 chr14 8956947 8957425 a 0 + 4 4 chr17 1575075 1580662 a 0 - 5 5 chr2 6559235 6564156 a 0 - 6 6 chr21 849656 857251 a 0 + 7 7 chr22 638017 640415 a 0 + 8 8 chr3 45619 54107 a 0 - 9 9 chr5 6543936 6551644 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1037818 | 1046797 | a | 0 | + | | chr1 | 4648965 | 4651695 | a | 0 | + | | chr2 | 6559235 | 6564156 | a | 0 | - | | chr3 | 45619 | 54107 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 8956947 | 8957425 | a | 0 | + | | chr17 | 1575075 | 1580662 | a | 0 | - | | chr21 | 849656 | 857251 | a | 0 | + | | chr22 | 638017 | 640415 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8789288 | 8794173 | a | 0 | + | | chr1 | 9338926 | 9344876 | a | 0 | + | | chr1 | 6775125 | 6782246 | a | 0 | + | | chr1 | 5565678 | 5574828 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 8137642 | 8142270 | a | 0 | - | | chr1 | 7563512 | 7567141 | a | 0 | - | | chr1 | 1932142 | 1932143 | a | 0 | - | | chr1 | 8303552 | 8308499 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmps_iqvrje/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1932142 1932143 a 0 - 1 1 chr1 5565678 5574828 a 0 - 2 2 chr1 6775125 6782246 a 0 + 3 3 chr1 7563512 7567141 a 0 - 4 4 chr1 8137642 8142270 a 0 - 5 5 chr1 8303552 8308499 a 0 - 6 6 chr1 8789288 8794173 a 0 + 7 7 chr1 9338926 9344876 a 0 + 8 8 chr15 237795 243271 a 0 + 9 9 chr16 5404877 5408506 a 0 + 10 10 chr7 3793612 3794450 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8789288 | 8794173 | a | 0 | + | | chr1 | 9338926 | 9344876 | a | 0 | + | | chr1 | 6775125 | 6782246 | a | 0 | + | | chr1 | 5565678 | 5574828 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 8137642 | 8142270 | a | 0 | - | | chr1 | 7563512 | 7567141 | a | 0 | - | | chr1 | 1932142 | 1932143 | a | 0 | - | | chr1 | 8303552 | 8308499 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8296776 | 8299909 | a | 0 | + | | chr1 | 8296776 | 8299277 | a | 0 | - | | chr1 | 8296776 | 8303469 | a | 0 | - | | chr19 | 4029349 | 4032609 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpv3o5f2rd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8296776 8299277 a 0 - 1 1 chr1 8296776 8299909 a 0 + 1 2 chr1 8296776 8303469 a 0 - 1 3 chr19 4029349 4032609 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8296776 | 8299909 | a | 0 | + | | chr1 | 8296776 | 8299277 | a | 0 | - | | chr1 | 8296776 | 8303469 | a | 0 | - | | chr19 | 4029349 | 4032609 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5758148 | 5766218 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbhdvc2d4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5758148 5766218 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5758148 | 5766218 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6091620 | 6097544 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_3tysehc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6091620 6097544 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6091620 | 6097544 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8000431 | 8001507 | a | 0 | + | | chr1 | 9130539 | 9131012 | a | 0 | - | | chr1 | 7440090 | 7449639 | a | 0 | - | | chr15 | 8080154 | 8083078 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpra4xlxuz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7440090 7449639 a 0 - 1 1 chr1 8000431 8001507 a 0 + 2 2 chr1 9130539 9131012 a 0 - 3 3 chr15 8080154 8083078 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8000431 | 8001507 | a | 0 | + | | chr1 | 9130539 | 9131012 | a | 0 | - | | chr1 | 7440090 | 7449639 | a | 0 | - | | chr15 | 8080154 | 8083078 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrX | 2998246 | 3007388 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpsxovp4te/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chrX 2998246 3007388 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrX | 2998246 | 3007388 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8354717 | 8356481 | a | 0 | + | | chr1 | 4657485 | 4661554 | a | 0 | + | | chr1 | 9435668 | 9442249 | a | 0 | + | | chr1 | 6715707 | 6725665 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 9959 | a | 0 | + | | chr1 | 8332836 | 8342794 | a | 0 | + | | chr1 | 4632653 | 4642611 | a | 0 | - | | chr1 | 1170794 | 1180149 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp6bg4vyo3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 9959 a 0 + 1 1 chr1 1170794 1180149 a 0 - 2 2 chr1 4632653 4642611 a 0 - 3 3 chr1 4657485 4661554 a 0 + 4 4 chr1 6715707 6725665 a 0 + 5 5 chr1 8332836 8342794 a 0 + 6 6 chr1 8354717 8356481 a 0 + 7 7 chr1 9435668 9442249 a 0 + 8 8 chr19 4632653 4634934 a 0 + 9 9 chr6 1456884 1458310 a 0 - 10 10 chr8 3072353 3082311 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8354717 | 8356481 | a | 0 | + | | chr1 | 4657485 | 4661554 | a | 0 | + | | chr1 | 9435668 | 9442249 | a | 0 | + | | chr1 | 6715707 | 6725665 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 9959 | a | 0 | + | | chr1 | 8332836 | 8342794 | a | 0 | + | | chr1 | 4632653 | 4642611 | a | 0 | - | | chr1 | 1170794 | 1180149 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2132226 | 2136579 | a | 0 | + | | chr1 | 3615844 | 3623384 | a | 0 | + | | chr1 | 5239636 | 5243401 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpcxi9ve8o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2132226 2136579 a 0 + 1 1 chr1 3615844 3623384 a 0 + 2 2 chr1 5239636 5243401 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2132226 | 2136579 | a | 0 | + | | chr1 | 3615844 | 3623384 | a | 0 | + | | chr1 | 5239636 | 5243401 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6178513 | 6186231 | a | 0 | + | | chr1 | 6178513 | 6185026 | a | 0 | - | | chr1 | 6178513 | 6185318 | a | 0 | - | | chr1 | 6178513 | 6180290 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 6178513 | 6185290 | a | 0 | - | | chr20 | 6094902 | 6101444 | a | 0 | - | | chr21 | 6178513 | 6182126 | a | 0 | + | | chrY | 6178513 | 6182564 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmps26rh0g8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2377180 2382388 a 0 - 1 1 chr1 6178513 6180290 a 0 - 2 2 chr1 6178513 6181228 a 0 - 2 3 chr1 6178513 6185026 a 0 - 2 4 chr1 6178513 6185318 a 0 - 2 5 chr1 6178513 6186231 a 0 + 2 6 chr10 6178513 6186686 a 0 + 3 7 chr18 6178513 6185290 a 0 - 4 8 chr20 6094902 6101444 a 0 - 5 9 chr21 6178513 6182126 a 0 + 6 10 chrY 6178513 6182564 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6178513 | 6186231 | a | 0 | + | | chr1 | 6178513 | 6185026 | a | 0 | - | | chr1 | 6178513 | 6185318 | a | 0 | - | | chr1 | 6178513 | 6180290 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 6178513 | 6185290 | a | 0 | - | | chr20 | 6094902 | 6101444 | a | 0 | - | | chr21 | 6178513 | 6182126 | a | 0 | + | | chrY | 6178513 | 6182564 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3525018 | 3532756 | a | 0 | + | | chr1 | 6920963 | 6928834 | a | 0 | + | | chr1 | 5843756 | 5847914 | a | 0 | + | | chr1 | 6920963 | 6925935 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9235810 | 9242467 | a | 0 | - | | chr1 | 7223008 | 7230259 | a | 0 | - | | chr1 | 6920963 | 6929681 | a | 0 | - | | chr1 | 6920963 | 6924948 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1qj7qapx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3525018 3532756 a 0 + 1 1 chr1 5843756 5847914 a 0 + 2 2 chr1 6920963 6921751 a 0 - 3 3 chr1 6920963 6924948 a 0 - 3 4 chr1 6920963 6925935 a 0 + 3 5 chr1 6920963 6928834 a 0 + 3 6 chr1 6920963 6929681 a 0 - 3 7 chr1 7223008 7230259 a 0 - 4 8 chr1 9235810 9242467 a 0 - 5 9 chr5 6920963 6925479 a 0 + 6 10 chrX 6920963 6929267 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3525018 | 3532756 | a | 0 | + | | chr1 | 6920963 | 6928834 | a | 0 | + | | chr1 | 5843756 | 5847914 | a | 0 | + | | chr1 | 6920963 | 6925935 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9235810 | 9242467 | a | 0 | - | | chr1 | 7223008 | 7230259 | a | 0 | - | | chr1 | 6920963 | 6929681 | a | 0 | - | | chr1 | 6920963 | 6924948 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5891002 | 5893202 | a | 0 | + | | chr17 | 8549582 | 8555035 | a | 0 | + | | chrX | 8451448 | 8457553 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpko7zmfph/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5891002 5893202 a 0 + 1 1 chr17 8549582 8555035 a 0 + 2 2 chrX 8451448 8457553 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5891002 | 5893202 | a | 0 | + | | chr17 | 8549582 | 8555035 | a | 0 | + | | chrX | 8451448 | 8457553 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1052370 | 1052716 | a | 0 | + | | chr1 | 2015739 | 2015775 | a | 0 | - | | chr1 | 9012910 | 9015948 | a | 0 | - | | chr1 | 4767124 | 4770162 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 3337515 | 3340553 | a | 0 | + | | chr18 | 3488343 | 3488677 | a | 0 | - | | chr22 | 9885608 | 9889526 | a | 0 | - | | chrM | 2015739 | 2018777 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp53m73d7l/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1052370 1052716 a 0 + 1 1 chr1 2015739 2015775 a 0 - 2 2 chr1 4767124 4770162 a 0 - 3 3 chr1 9012910 9015948 a 0 - 4 4 chr11 3337515 3340553 a 0 + 5 5 chr18 3488343 3488677 a 0 - 6 6 chr22 9885608 9889526 a 0 - 7 7 chr3 7045944 7055157 a 0 - 8 8 chr4 5209906 5218938 a 0 - 9 9 chr9 1154953 1157991 a 0 + 10 10 chrM 2015739 2018777 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1052370 | 1052716 | a | 0 | + | | chr1 | 2015739 | 2015775 | a | 0 | - | | chr1 | 9012910 | 9015948 | a | 0 | - | | chr1 | 4767124 | 4770162 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 3337515 | 3340553 | a | 0 | + | | chr18 | 3488343 | 3488677 | a | 0 | - | | chr22 | 9885608 | 9889526 | a | 0 | - | | chrM | 2015739 | 2018777 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 3580945 | 3583818 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmps8xdyd25/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr10 3580945 3583818 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 3580945 | 3583818 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1925217 | 1933620 | a | 0 | + | | chr22 | 8545516 | 8546878 | a | 0 | + | | chr22 | 8727520 | 8727825 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbcqmbwds/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1925217 1933620 a 0 + 1 1 chr22 8545516 8546878 a 0 + 2 2 chr22 8727520 8727825 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1925217 | 1933620 | a | 0 | + | | chr22 | 8545516 | 8546878 | a | 0 | + | | chr22 | 8727520 | 8727825 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5002758 | 5008736 | a | 0 | + | | chr1 | 5827185 | 5834093 | a | 0 | + | | chr1 | 1120836 | 1127006 | a | 0 | - | | chr1 | 3708224 | 3717176 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 1504172 | 1513583 | a | 0 | - | | chr19 | 8943169 | 8952134 | a | 0 | - | | chr21 | 7649096 | 7649564 | a | 0 | - | | chrX | 1924144 | 1927982 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpawuw81ia/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1120836 1127006 a 0 - 1 1 chr1 3708224 3717176 a 0 - 2 2 chr1 5002758 5008736 a 0 + 3 3 chr1 5827185 5834093 a 0 + 4 4 chr1 6078459 6084096 a 0 - 5 5 chr1 6089742 6090466 a 0 - 6 6 chr18 1504172 1513583 a 0 - 7 7 chr19 8943169 8952134 a 0 - 8 8 chr21 7649096 7649564 a 0 - 9 9 chr4 38352 44505 a 0 + 10 10 chrX 1924144 1927982 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5002758 | 5008736 | a | 0 | + | | chr1 | 5827185 | 5834093 | a | 0 | + | | chr1 | 1120836 | 1127006 | a | 0 | - | | chr1 | 3708224 | 3717176 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 1504172 | 1513583 | a | 0 | - | | chr19 | 8943169 | 8952134 | a | 0 | - | | chr21 | 7649096 | 7649564 | a | 0 | - | | chrX | 1924144 | 1927982 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9135487 | 9139416 | a | 0 | + | | chr1 | 9999999 | 10004687 | a | 0 | + | | chr1 | 690070 | 697333 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpcmga0ek6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 690070 697333 a 0 - 1 1 chr1 9135487 9139416 a 0 + 2 2 chr1 9999999 10004687 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9135487 | 9139416 | a | 0 | + | | chr1 | 9999999 | 10004687 | a | 0 | + | | chr1 | 690070 | 697333 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr16 | 1215627 | 1215628 | a | 0 | + | | chr17 | 4342932 | 4347943 | a | 0 | + | | chr19 | 2197971 | 2207671 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpw44s03c5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr16 1215627 1215628 a 0 + 1 1 chr17 4342932 4347943 a 0 + 2 2 chr19 2197971 2207671 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr16 | 1215627 | 1215628 | a | 0 | + | | chr17 | 4342932 | 4347943 | a | 0 | + | | chr19 | 2197971 | 2207671 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10000724 | a | 0 | + | | chr1 | 9486555 | 9496328 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpoa7sjv92/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9486555 9496328 a 0 + 1 1 chr1 10000000 10000724 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10000724 | a | 0 | + | | chr1 | 9486555 | 9496328 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5284490 | 5291955 | a | 0 | + | | chr1 | 7041012 | 7049125 | a | 0 | + | | chr1 | 9062284 | 9064665 | a | 0 | + | | chr1 | 8484377 | 8488930 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 4512499 | 4519254 | a | 0 | + | | chr15 | 5142203 | 5148083 | a | 0 | + | | chr18 | 7416479 | 7416481 | a | 0 | - | | chr20 | 3063575 | 3070048 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpntlz_krm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 277889 286002 a 0 + 1 1 chr1 5284490 5291955 a 0 + 2 2 chr1 6141121 6148467 a 0 - 3 3 chr1 7041012 7049125 a 0 + 4 4 chr1 8484377 8488930 a 0 + 5 5 chr1 9062284 9064665 a 0 + 6 6 chr10 4512499 4519254 a 0 + 7 7 chr15 5142203 5148083 a 0 + 8 8 chr18 7416479 7416481 a 0 - 9 9 chr20 3063575 3070048 a 0 - 10 10 chr8 8374549 8375895 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5284490 | 5291955 | a | 0 | + | | chr1 | 7041012 | 7049125 | a | 0 | + | | chr1 | 9062284 | 9064665 | a | 0 | + | | chr1 | 8484377 | 8488930 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 4512499 | 4519254 | a | 0 | + | | chr15 | 5142203 | 5148083 | a | 0 | + | | chr18 | 7416479 | 7416481 | a | 0 | - | | chr20 | 3063575 | 3070048 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4533682 | 4535689 | a | 0 | - | | chrY | 4533682 | 4541262 | a | 0 | - | | chrY | 4533682 | 4543682 | a | 0 | - | | chrY | 4533682 | 4542784 | a | 0 | - | | chrY | 5637400 | 5646595 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpisl0ob23/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4533682 4535689 a 0 - 1 1 chrY 4533682 4541262 a 0 - 2 2 chrY 4533682 4542784 a 0 - 2 3 chrY 4533682 4543682 a 0 - 2 4 chrY 5637400 5646595 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4533682 | 4535689 | a | 0 | - | | chrY | 4533682 | 4541262 | a | 0 | - | | chrY | 4533682 | 4543682 | a | 0 | - | | chrY | 4533682 | 4542784 | a | 0 | - | | chrY | 5637400 | 5646595 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7033835 | 7038195 | a | 0 | + | | chr11 | 311383 | 312330 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp4ny3sphr/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7033835 7038195 a 0 + 1 1 chr11 311383 312330 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7033835 | 7038195 | a | 0 | + | | chr11 | 311383 | 312330 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6772659 | 6782659 | a | 0 | + | | chr1 | 1260455 | 1260839 | a | 0 | + | | chr1 | 1869573 | 1870240 | a | 0 | + | | chr1 | 7511479 | 7513165 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 5296940 | 5306940 | a | 0 | + | | chr15 | 10000000 | 10002405 | a | 0 | + | | chr16 | 960950 | 965483 | a | 0 | - | | chr17 | 734114 | 734951 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7o05mj51/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 179817 181660 a 0 - 1 1 chr1 1260455 1260839 a 0 + 2 2 chr1 1869573 1870240 a 0 + 3 3 chr1 6244100 6249002 a 0 + 4 4 chr1 6772659 6782659 a 0 + 5 5 chr1 7511479 7513165 a 0 + 6 6 chr1 8150339 8157194 a 0 - 7 7 chr15 10000000 10002405 a 0 + 8 8 chr16 960950 965483 a 0 - 9 9 chr17 734114 734951 a 0 + 10 10 chr6 5296940 5306940 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6772659 | 6782659 | a | 0 | + | | chr1 | 1260455 | 1260839 | a | 0 | + | | chr1 | 1869573 | 1870240 | a | 0 | + | | chr1 | 7511479 | 7513165 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 5296940 | 5306940 | a | 0 | + | | chr15 | 10000000 | 10002405 | a | 0 | + | | chr16 | 960950 | 965483 | a | 0 | - | | chr17 | 734114 | 734951 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1892881 | 1894093 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpw948o0pd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1892881 1894093 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1892881 | 1894093 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8830065 | 8836935 | a | 0 | + | | chr1 | 1578860 | 1585394 | a | 0 | + | | chr1 | 9964060 | 9970350 | a | 0 | + | | chr1 | 1 | 4710 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 4710 | a | 0 | + | | chr1 | 9342774 | 9342851 | a | 0 | - | | chr1 | 2208985 | 2218887 | a | 0 | - | | chr1 | 1381078 | 1387312 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmprfegkikj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4710 a 0 + 1 1 chr1 1381078 1387312 a 0 - 2 2 chr1 1578860 1585394 a 0 + 3 3 chr1 2208985 2218887 a 0 - 4 4 chr1 8830065 8836935 a 0 + 5 5 chr1 9342774 9342851 a 0 - 6 6 chr1 9964060 9970350 a 0 + 7 7 chr17 8540834 8541269 a 0 - 8 8 chr4 6638712 6644547 a 0 - 9 9 chr8 4927567 4934101 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8830065 | 8836935 | a | 0 | + | | chr1 | 1578860 | 1585394 | a | 0 | + | | chr1 | 9964060 | 9970350 | a | 0 | + | | chr1 | 1 | 4710 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 4710 | a | 0 | + | | chr1 | 9342774 | 9342851 | a | 0 | - | | chr1 | 2208985 | 2218887 | a | 0 | - | | chr1 | 1381078 | 1387312 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6156920 | 6164998 | a | 0 | + | | chr1 | 9783724 | 9791296 | a | 0 | + | | chr1 | 4913440 | 4919509 | a | 0 | + | | chr17 | 10000000 | 10009649 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpp8um58ei/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4913440 4919509 a 0 + 1 1 chr1 6156920 6164998 a 0 + 2 2 chr1 9783724 9791296 a 0 + 3 3 chr17 10000000 10009649 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6156920 | 6164998 | a | 0 | + | | chr1 | 9783724 | 9791296 | a | 0 | + | | chr1 | 4913440 | 4919509 | a | 0 | + | | chr17 | 10000000 | 10009649 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2911542 | 2920471 | a | 0 | - | | chr5 | 3919459 | 3927172 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpdsai5rnz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2911542 2920471 a 0 - 1 1 chr5 3919459 3927172 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2911542 | 2920471 | a | 0 | - | | chr5 | 3919459 | 3927172 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1315188 | 1320717 | a | 0 | + | | chr1 | 1233024 | 1234271 | a | 0 | - | | chr1 | 2755973 | 2765506 | a | 0 | - | | chr1 | 8945500 | 8945501 | a | 0 | - | | chr1 | 7458990 | 7468523 | a | 0 | - | | chr10 | 6361869 | 6371402 | a | 0 | - | | chrM | 753913 | 763446 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp925wyz39/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1233024 1234271 a 0 - 1 1 chr1 1315188 1320717 a 0 + 2 2 chr1 2755973 2765506 a 0 - 3 3 chr1 7458990 7468523 a 0 - 4 4 chr1 8945500 8945501 a 0 - 5 5 chr10 6361869 6371402 a 0 - 6 6 chrM 753913 763446 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1315188 | 1320717 | a | 0 | + | | chr1 | 1233024 | 1234271 | a | 0 | - | | chr1 | 2755973 | 2765506 | a | 0 | - | | chr1 | 8945500 | 8945501 | a | 0 | - | | chr1 | 7458990 | 7468523 | a | 0 | - | | chr10 | 6361869 | 6371402 | a | 0 | - | | chrM | 753913 | 763446 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6731637 | 6739832 | a | 0 | + | | chr1 | 8821784 | 8823394 | a | 0 | + | | chr1 | 3483798 | 3486604 | a | 0 | - | | chr7 | 5650557 | 5657392 | a | 0 | - | | chr11 | 9339909 | 9342595 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpb3xhx5oy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3483798 3486604 a 0 - 1 1 chr1 6731637 6739832 a 0 + 2 2 chr1 8821784 8823394 a 0 + 3 3 chr11 9339909 9342595 a 0 + 4 4 chr7 5650557 5657392 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6731637 | 6739832 | a | 0 | + | | chr1 | 8821784 | 8823394 | a | 0 | + | | chr1 | 3483798 | 3486604 | a | 0 | - | | chr7 | 5650557 | 5657392 | a | 0 | - | | chr11 | 9339909 | 9342595 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3332815 | 3334391 | a | 0 | - | | chr1 | 6483359 | 6487655 | a | 0 | - | | chr1 | 1968332 | 1968717 | a | 0 | - | | chr1 | 21087 | 21715 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 7512888 | 7515430 | a | 0 | + | | chr22 | 284858 | 288071 | a | 0 | - | | chrM | 2286662 | 2294034 | a | 0 | + | | chrX | 9401139 | 9404130 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpd00mgdtm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 21087 21715 a 0 - 1 1 chr1 1968332 1968717 a 0 - 2 2 chr1 3332815 3334391 a 0 - 3 3 chr1 6483359 6487655 a 0 - 4 4 chr13 9142241 9145454 a 0 - 5 5 chr14 7512888 7515430 a 0 + 6 6 chr22 284858 288071 a 0 - 7 7 chr4 9999999 10007233 a 0 - 8 8 chr9 9401139 9404352 a 0 - 9 9 chrM 2286662 2294034 a 0 + 10 10 chrX 9401139 9404130 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3332815 | 3334391 | a | 0 | - | | chr1 | 6483359 | 6487655 | a | 0 | - | | chr1 | 1968332 | 1968717 | a | 0 | - | | chr1 | 21087 | 21715 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 7512888 | 7515430 | a | 0 | + | | chr22 | 284858 | 288071 | a | 0 | - | | chrM | 2286662 | 2294034 | a | 0 | + | | chrX | 9401139 | 9404130 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3259150 | 3265136 | a | 0 | - | | chr7 | 1065224 | 1073557 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp3hpowuta/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3259150 3265136 a 0 - 1 1 chr7 1065224 1073557 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3259150 | 3265136 | a | 0 | - | | chr7 | 1065224 | 1073557 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2132048 | 2141124 | a | 0 | + | | chr1 | 609280 | 614180 | a | 0 | + | | chr10 | 8276420 | 8281320 | a | 0 | - | | chr22 | 609280 | 615451 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpjf1zszs2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 609280 614180 a 0 + 1 1 chr1 2132048 2141124 a 0 + 2 2 chr10 8276420 8281320 a 0 - 3 3 chr22 609280 615451 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2132048 | 2141124 | a | 0 | + | | chr1 | 609280 | 614180 | a | 0 | + | | chr10 | 8276420 | 8281320 | a | 0 | - | | chr22 | 609280 | 615451 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 6797253 | 6799887 | a | 0 | + | | chr5 | 2928319 | 2930399 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpg7s7jxed/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr5 2928319 2930399 a 0 - 1 1 chr5 6797253 6799887 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 6797253 | 6799887 | a | 0 | + | | chr5 | 2928319 | 2930399 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4204253 | 4208559 | a | 0 | + | | chr1 | 8015605 | 8022700 | a | 0 | + | | chr1 | 9573238 | 9580832 | a | 0 | + | | chr1 | 3674211 | 3681805 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr21 | 7915333 | 7915335 | a | 0 | + | | chr21 | 4614767 | 4616083 | a | 0 | - | | chr21 | 9699773 | 9707324 | a | 0 | - | | chr21 | 20086 | 25614 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpztjs4t8p/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3674211 3681805 a 0 - 1 1 chr1 4204253 4208559 a 0 + 2 2 chr1 8015605 8022700 a 0 + 3 3 chr1 9573238 9580832 a 0 + 4 4 chr11 6351841 6361322 a 0 - 5 5 chr21 20086 25614 a 0 - 6 6 chr21 2530763 2538357 a 0 + 7 7 chr21 4614767 4616083 a 0 - 8 8 chr21 7915333 7915335 a 0 + 9 9 chr21 8673540 8681134 a 0 + 10 10 chr21 9699773 9707324 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4204253 | 4208559 | a | 0 | + | | chr1 | 8015605 | 8022700 | a | 0 | + | | chr1 | 9573238 | 9580832 | a | 0 | + | | chr1 | 3674211 | 3681805 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr21 | 7915333 | 7915335 | a | 0 | + | | chr21 | 4614767 | 4616083 | a | 0 | - | | chr21 | 9699773 | 9707324 | a | 0 | - | | chr21 | 20086 | 25614 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6313491 | 6318021 | a | 0 | + | | chr1 | 3923291 | 3927821 | a | 0 | + | | chr11 | 9828921 | 9833451 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2i6zi5ya/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3923291 3927821 a 0 + 1 1 chr1 6313491 6318021 a 0 + 2 2 chr11 9828921 9833451 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6313491 | 6318021 | a | 0 | + | | chr1 | 3923291 | 3927821 | a | 0 | + | | chr11 | 9828921 | 9833451 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3653453 | 3658167 | a | 0 | - | | chr1 | 9828696 | 9832403 | a | 0 | - | | chr1 | 5624015 | 5626882 | a | 0 | - | | chrY | 8164500 | 8167719 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmps_zplt4g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3653453 3658167 a 0 - 1 1 chr1 5624015 5626882 a 0 - 2 2 chr1 9828696 9832403 a 0 - 3 3 chrY 8164500 8167719 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3653453 | 3658167 | a | 0 | - | | chr1 | 9828696 | 9832403 | a | 0 | - | | chr1 | 5624015 | 5626882 | a | 0 | - | | chrY | 8164500 | 8167719 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 746268 | 752759 | a | 0 | + | | chr1 | 2522543 | 2531648 | a | 0 | + | | chr1 | 8185027 | 8188699 | a | 0 | + | | chr1 | 2312834 | 2322626 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 2522543 | 2523618 | a | 0 | - | | chr11 | 5476290 | 5476291 | a | 0 | + | | chr16 | 2522543 | 2528730 | a | 0 | - | | chr16 | 3892936 | 3901046 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpor5k6vj_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 746268 752759 a 0 + 1 1 chr1 1467198 1471196 a 0 - 2 2 chr1 2312834 2322626 a 0 + 3 3 chr1 2522543 2531648 a 0 + 4 4 chr1 5480200 5480944 a 0 - 5 5 chr1 8185027 8188699 a 0 + 6 6 chr10 2522543 2523618 a 0 - 7 7 chr11 5476290 5476291 a 0 + 8 8 chr16 2522543 2528730 a 0 - 9 9 chr16 3892936 3901046 a 0 - 10 10 chr6 2522543 2524767 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 746268 | 752759 | a | 0 | + | | chr1 | 2522543 | 2531648 | a | 0 | + | | chr1 | 8185027 | 8188699 | a | 0 | + | | chr1 | 2312834 | 2322626 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 2522543 | 2523618 | a | 0 | - | | chr11 | 5476290 | 5476291 | a | 0 | + | | chr16 | 2522543 | 2528730 | a | 0 | - | | chr16 | 3892936 | 3901046 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 2200122 | 2205400 | a | 0 | + | | chr5 | 448151 | 452975 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpjeut3_ma/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr2 2200122 2205400 a 0 + 1 1 chr5 448151 452975 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 2200122 | 2205400 | a | 0 | + | | chr5 | 448151 | 452975 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 1060604 | 1061502 | a | 0 | + | | chr21 | 9473269 | 9476560 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0daxxtyy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr13 1060604 1061502 a 0 + 1 1 chr21 9473269 9476560 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 1060604 | 1061502 | a | 0 | + | | chr21 | 9473269 | 9476560 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 368590 | 371578 | a | 0 | + | | chr1 | 9362944 | 9370087 | a | 0 | + | | chr1 | 4006678 | 4014830 | a | 0 | - | | chr1 | 4588763 | 4595165 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 6917268 | 6924531 | a | 0 | + | | chr19 | 6967908 | 6977548 | a | 0 | + | | chr21 | 6992218 | 6992220 | a | 0 | + | | chr22 | 6740810 | 6750810 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpl4n1pp6m/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 368590 371578 a 0 + 1 1 chr1 4006678 4014830 a 0 - 2 2 chr1 4034280 4044037 a 0 - 3 3 chr1 4588763 4595165 a 0 - 4 4 chr1 9362944 9370087 a 0 + 5 5 chr11 6917268 6924531 a 0 + 6 6 chr19 6967908 6977548 a 0 + 7 7 chr2 8885425 8892358 a 0 + 8 8 chr21 6992218 6992220 a 0 + 9 9 chr22 6740810 6750810 a 0 - 10 10 chr3 4452315 4453664 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 368590 | 371578 | a | 0 | + | | chr1 | 9362944 | 9370087 | a | 0 | + | | chr1 | 4006678 | 4014830 | a | 0 | - | | chr1 | 4588763 | 4595165 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 6917268 | 6924531 | a | 0 | + | | chr19 | 6967908 | 6977548 | a | 0 | + | | chr21 | 6992218 | 6992220 | a | 0 | + | | chr22 | 6740810 | 6750810 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 772355 | 775005 | a | 0 | + | | chr1 | 772355 | 779082 | a | 0 | + | | chr1 | 772355 | 781182 | a | 0 | + | | chr1 | 6938866 | 6940584 | a | 0 | - | | chr5 | 772355 | 775900 | a | 0 | - | | chr10 | 772355 | 775118 | a | 0 | + | | chrY | 772355 | 776788 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpukiajic1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 772355 775005 a 0 + 1 1 chr1 772355 779082 a 0 + 1 2 chr1 772355 781182 a 0 + 1 3 chr1 6938866 6940584 a 0 - 2 4 chr10 772355 775118 a 0 + 3 5 chr5 772355 775900 a 0 - 4 6 chrY 772355 776788 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 772355 | 775005 | a | 0 | + | | chr1 | 772355 | 779082 | a | 0 | + | | chr1 | 772355 | 781182 | a | 0 | + | | chr1 | 6938866 | 6940584 | a | 0 | - | | chr5 | 772355 | 775900 | a | 0 | - | | chr10 | 772355 | 775118 | a | 0 | + | | chrY | 772355 | 776788 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10005729 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmph0w_neak/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 10000000 10005729 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10005729 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6938028 | 6938799 | a | 0 | + | | chr1 | 8155951 | 8160282 | a | 0 | + | | chr1 | 1456167 | 1463192 | a | 0 | - | | chr1 | 9075213 | 9075215 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 4241480 | 4251242 | a | 0 | - | | chr1 | 9616217 | 9616846 | a | 0 | - | | chr1 | 5152962 | 5157696 | a | 0 | - | | chr1 | 7514055 | 7514675 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpixv157w_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 172601 180868 a 0 - 1 1 chr1 1456167 1463192 a 0 - 2 2 chr1 4241480 4251242 a 0 - 3 3 chr1 4256251 4262482 a 0 - 4 4 chr1 5152962 5157696 a 0 - 5 5 chr1 5969238 5976857 a 0 - 6 6 chr1 6938028 6938799 a 0 + 7 7 chr1 7514055 7514675 a 0 - 8 8 chr1 8155951 8160282 a 0 + 9 9 chr1 9075213 9075215 a 0 - 10 10 chr1 9616217 9616846 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6938028 | 6938799 | a | 0 | + | | chr1 | 8155951 | 8160282 | a | 0 | + | | chr1 | 1456167 | 1463192 | a | 0 | - | | chr1 | 9075213 | 9075215 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 4241480 | 4251242 | a | 0 | - | | chr1 | 9616217 | 9616846 | a | 0 | - | | chr1 | 5152962 | 5157696 | a | 0 | - | | chr1 | 7514055 | 7514675 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4668773 | 4675777 | a | 0 | + | | chr1 | 4668773 | 4675777 | a | 0 | + | | chr1 | 4668773 | 4675777 | a | 0 | - | | chr1 | 4668773 | 4675777 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 4668773 | 4668795 | a | 0 | - | | chr11 | 4142998 | 4150002 | a | 0 | - | | chr18 | 4668773 | 4675777 | a | 0 | - | | chrX | 4668773 | 4675777 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpvw2u7w8n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4668773 4675777 a 0 + 1 1 chr1 4668773 4675777 a 0 + 1 2 chr1 4668773 4675777 a 0 - 1 3 chr1 4668773 4675777 a 0 - 1 4 chr11 4142998 4150002 a 0 - 2 5 chr18 4668773 4675777 a 0 - 3 6 chr3 4668773 4673040 a 0 - 4 7 chr4 4668773 4678384 a 0 - 5 8 chr8 9882614 9885236 a 0 + 6 9 chr9 4668773 4668795 a 0 - 7 10 chrX 4668773 4675777 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4668773 | 4675777 | a | 0 | + | | chr1 | 4668773 | 4675777 | a | 0 | + | | chr1 | 4668773 | 4675777 | a | 0 | - | | chr1 | 4668773 | 4675777 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 4668773 | 4668795 | a | 0 | - | | chr11 | 4142998 | 4150002 | a | 0 | - | | chr18 | 4668773 | 4675777 | a | 0 | - | | chrX | 4668773 | 4675777 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8212140 | 8214353 | a | 0 | + | | chrM | 6117588 | 6121525 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpd9xe795h/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8212140 8214353 a 0 + 1 1 chrM 6117588 6121525 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8212140 | 8214353 | a | 0 | + | | chrM | 6117588 | 6121525 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 224372 | 229792 | a | 0 | + | | chr1 | 1418218 | 1418220 | a | 0 | + | | chr1 | 9656852 | 9660300 | a | 0 | + | | chr1 | 7820918 | 7827903 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2912396 | 2913088 | a | 0 | - | | chr1 | 694620 | 695504 | a | 0 | - | | chr1 | 9527054 | 9527649 | a | 0 | - | | chr1 | 9656852 | 9661120 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpadb1mpuy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 224372 229792 a 0 + 1 1 chr1 694620 695504 a 0 - 2 2 chr1 1418218 1418220 a 0 + 3 3 chr1 2912396 2913088 a 0 - 4 4 chr1 7820918 7827903 a 0 + 5 5 chr1 9527054 9527649 a 0 - 6 6 chr1 9656852 9660300 a 0 + 7 7 chr1 9656852 9661120 a 0 - 7 8 chr2 7637741 7646033 a 0 + 8 9 chr20 8558364 8568251 a 0 - 9 10 chrX 8149580 8159504 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 224372 | 229792 | a | 0 | + | | chr1 | 1418218 | 1418220 | a | 0 | + | | chr1 | 9656852 | 9660300 | a | 0 | + | | chr1 | 7820918 | 7827903 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2912396 | 2913088 | a | 0 | - | | chr1 | 694620 | 695504 | a | 0 | - | | chr1 | 9527054 | 9527649 | a | 0 | - | | chr1 | 9656852 | 9661120 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 934623 | 938847 | a | 0 | + | | chr1 | 2034043 | 2038267 | a | 0 | + | | chr1 | 1145042 | 1149266 | a | 0 | + | | chr1 | 130450 | 133011 | a | 0 | - | | chr21 | 1 | 4193 | a | 0 | - | | chrM | 5887174 | 5895555 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpy9eireh_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 130450 133011 a 0 - 1 1 chr1 934623 938847 a 0 + 2 2 chr1 1145042 1149266 a 0 + 3 3 chr1 2034043 2038267 a 0 + 4 4 chr21 1 4193 a 0 - 5 5 chrM 5887174 5895555 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 934623 | 938847 | a | 0 | + | | chr1 | 2034043 | 2038267 | a | 0 | + | | chr1 | 1145042 | 1149266 | a | 0 | + | | chr1 | 130450 | 133011 | a | 0 | - | | chr21 | 1 | 4193 | a | 0 | - | | chrM | 5887174 | 5895555 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9928262 | 9935286 | a | 0 | - | | chr12 | 9618534 | 9619053 | a | 0 | + | | chrM | 6943832 | 6946321 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbd4m__wg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9928262 9935286 a 0 - 1 1 chr12 9618534 9619053 a 0 + 2 2 chrM 6943832 6946321 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9928262 | 9935286 | a | 0 | - | | chr12 | 9618534 | 9619053 | a | 0 | + | | chrM | 6943832 | 6946321 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1682863 | 1685408 | a | 0 | + | | chr1 | 1682863 | 1685408 | a | 0 | + | | chr13 | 646108 | 648653 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp6qefxdl5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1682863 1685408 a 0 + 1 1 chr1 1682863 1685408 a 0 + 1 2 chr13 646108 648653 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1682863 | 1685408 | a | 0 | + | | chr1 | 1682863 | 1685408 | a | 0 | + | | chr13 | 646108 | 648653 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1731713 | 1739792 | a | 0 | + | | chr1 | 7033572 | 7041935 | a | 0 | + | | chr1 | 1 | 8803 | a | 0 | + | | chr1 | 9573527 | 9581890 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9573527 | 9581890 | a | 0 | + | | chr1 | 2091490 | 2091492 | a | 0 | + | | chr1 | 2581724 | 2590087 | a | 0 | + | | chr1 | 4345220 | 4353583 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7ojakb28/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 8803 a 0 + 1 1 chr1 1731713 1739792 a 0 + 2 2 chr1 2091490 2091492 a 0 + 3 3 chr1 2581724 2590087 a 0 + 4 4 chr1 4345220 4353583 a 0 - 5 5 chr1 7033572 7041935 a 0 + 6 6 chr1 9573527 9581890 a 0 + 7 7 chr20 2637223 2645586 a 0 - 8 8 chr7 2393605 2401968 a 0 - 9 9 chrY 1321655 1331320 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1731713 | 1739792 | a | 0 | + | | chr1 | 7033572 | 7041935 | a | 0 | + | | chr1 | 1 | 8803 | a | 0 | + | | chr1 | 9573527 | 9581890 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9573527 | 9581890 | a | 0 | + | | chr1 | 2091490 | 2091492 | a | 0 | + | | chr1 | 2581724 | 2590087 | a | 0 | + | | chr1 | 4345220 | 4353583 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8350701 | 8357812 | a | 0 | + | | chr1 | 431956 | 433270 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmps9xws998/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 431956 433270 a 0 + 1 1 chr1 8350701 8357812 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8350701 | 8357812 | a | 0 | + | | chr1 | 431956 | 433270 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5676227 | 5682657 | a | 0 | + | | chr1 | 2434459 | 2435684 | a | 0 | - | | chr2 | 2434459 | 2438927 | a | 0 | + | | chr8 | 2434459 | 2434621 | a | 0 | - | | chr22 | 2434459 | 2434621 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpgstkyrcu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2434459 2435684 a 0 - 1 1 chr1 5676227 5682657 a 0 + 2 2 chr2 2434459 2438927 a 0 + 3 3 chr22 2434459 2434621 a 0 + 4 4 chr8 2434459 2434621 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5676227 | 5682657 | a | 0 | + | | chr1 | 2434459 | 2435684 | a | 0 | - | | chr2 | 2434459 | 2438927 | a | 0 | + | | chr8 | 2434459 | 2434621 | a | 0 | - | | chr22 | 2434459 | 2434621 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3809813 | 3810667 | a | 0 | + | | chr1 | 5368315 | 5369169 | a | 0 | - | | chr1 | 8522436 | 8523290 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0dezwbf6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3809813 3810667 a 0 + 1 1 chr1 5368315 5369169 a 0 - 2 2 chr1 8522436 8523290 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3809813 | 3810667 | a | 0 | + | | chr1 | 5368315 | 5369169 | a | 0 | - | | chr1 | 8522436 | 8523290 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7810673 | 7811889 | a | 0 | + | | chr1 | 6590890 | 6593352 | a | 0 | + | | chr1 | 1081983 | 1084074 | a | 0 | + | | chr1 | 812822 | 814913 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr16 | 3755611 | 3757702 | a | 0 | + | | chr18 | 4919579 | 4921670 | a | 0 | + | | chr21 | 7282038 | 7284129 | a | 0 | + | | chr22 | 2399908 | 2407494 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpe5czrc3a/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 812822 814913 a 0 - 1 1 chr1 1081983 1084074 a 0 + 2 2 chr1 6590890 6593352 a 0 + 3 3 chr1 7810673 7811889 a 0 + 4 4 chr10 336541 345291 a 0 + 5 5 chr16 3755611 3757702 a 0 + 6 6 chr18 4919579 4921670 a 0 + 7 7 chr21 7282038 7284129 a 0 + 8 8 chr22 2399908 2407494 a 0 + 9 9 chr3 7593224 7595315 a 0 + 10 10 chr5 8653297 8655388 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7810673 | 7811889 | a | 0 | + | | chr1 | 6590890 | 6593352 | a | 0 | + | | chr1 | 1081983 | 1084074 | a | 0 | + | | chr1 | 812822 | 814913 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr16 | 3755611 | 3757702 | a | 0 | + | | chr18 | 4919579 | 4921670 | a | 0 | + | | chr21 | 7282038 | 7284129 | a | 0 | + | | chr22 | 2399908 | 2407494 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp88z8gv1f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. _________________________________ test_windows _________________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 @pytest.mark.bedtools > @settings( max_examples=max_examples, print_blob=True, deadline=deadline, suppress_health_check=HealthCheck.all()) tests/test_unary.py:230: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:259: in test_windows result = gr.window(10)["Chromosome Start End".split()].unstrand() pyranges/pyranges.py:5485: in window df = pyrange_apply_single(_windows, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:11: in _windows idxs, starts, ends = makewindows(df.index.values, df.Start.values, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_windows( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBAAAADIAAw==') as a decorator on your test case sorted_nearest/src/windows.pyx:20: Exception ----------------------------- Captured stdout call ----------------------------- bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp1vl53u8j/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpo40gwx6z/f1.bed) bedtools_df Chromosome Start End 0 chr16 5214731 5214741 1 chr16 5214741 5214751 2 chr16 5214751 5214761 3 chr16 5214761 5214771 4 chr16 5214771 5214781 .. ... ... ... 826 chr22 9927763 9927773 827 chr22 9927773 9927783 828 chr22 9927783 9927793 829 chr22 9927793 9927803 830 chr22 9927803 9927811 [831 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpx3sa96tf/f1.bed) bedtools_df Chromosome Start End 0 chr1 786689 786699 1 chr1 786699 786709 2 chr1 786709 786719 3 chr1 786719 786729 4 chr1 786729 786739 .. ... ... ... 713 chr1 790229 790239 714 chr1 790239 790249 715 chr1 790249 790259 716 chr1 790259 790269 717 chr1 790269 790274 [718 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmputic5_oo/f1.bed) bedtools_df Chromosome Start End 0 chr1 65547 65557 1 chr1 65557 65567 2 chr1 65567 65577 3 chr1 65577 65587 4 chr1 65587 65597 .. ... ... ... 794 chr16 51825 51835 795 chr16 51835 51845 796 chr16 51845 51855 797 chr16 51855 51865 798 chr16 51865 51869 [799 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8g13vgvu/f1.bed) bedtools_df Chromosome Start End 0 chr1 44335 44345 1 chr1 44345 44355 2 chr1 44355 44365 3 chr1 44365 44375 4 chr1 44375 44385 .. ... ... ... 794 chr1 65947 65957 795 chr1 65957 65967 796 chr1 65967 65977 797 chr1 65977 65987 798 chr1 65987 65988 [799 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpuls85vm7/f1.bed) bedtools_df Chromosome Start End 0 chr1 44335 44345 1 chr1 44345 44355 2 chr1 44355 44365 3 chr1 44365 44375 4 chr1 44375 44385 .. ... ... ... 794 chr1 65947 65957 795 chr1 65957 65967 796 chr1 65967 65977 797 chr1 65977 65987 798 chr1 65987 65988 [799 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3nium81y/f1.bed) bedtools_df Chromosome Start End 0 chr1 3014913 3014915 1 chr1 3014913 3014923 2 chr1 3014923 3014933 3 chr1 3014933 3014943 4 chr1 3014943 3014953 .. ... ... ... 827 chr11 3015633 3015643 828 chr11 3015643 3015653 829 chr11 3015653 3015663 830 chr11 3015663 3015673 831 chr11 3015673 3015682 [832 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpj4vf29yv/f1.bed) bedtools_df Chromosome Start End 0 chr1 11567 11569 1 chr1 72451 72453 2 chr1 79876 79886 3 chr1 79886 79896 4 chr1 79896 79906 .. ... ... ... 751 chr1 87366 87376 752 chr1 87376 87386 753 chr1 87386 87396 754 chr1 87396 87406 755 chr1 87406 87410 [756 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv2d8mjwe/f1.bed) bedtools_df Chromosome Start End 0 chr1 5483293 5483303 1 chr1 5483303 5483313 2 chr1 5483313 5483323 3 chr1 5483323 5483333 4 chr1 5483333 5483343 ... ... ... ... 1277 chr19 5955774 5955784 1278 chr19 5955784 5955794 1279 chr19 5955794 5955804 1280 chr19 5955804 5955814 1281 chr19 5955814 5955824 [1282 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpufozilvv/f1.bed) bedtools_df Chromosome Start End 0 chr1 1645852 1645862 1 chr1 1645862 1645866 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8hz9dsjn/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv5edghkg/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplh6xq8jz/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpw470pbbu/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpku613qw4/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2_uhm3cd/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpos_ybyh8/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpn866ryss/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpuxjxzyi1/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpufzhl7sx/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3lmvvp39/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0doz07hv/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmphvbe6w5f/f1.bed) bedtools_df Chromosome Start End 0 chr1 1011980 1011990 1 chr1 1011990 1012000 2 chr1 1012000 1012010 3 chr1 1012010 1012020 4 chr1 1012020 1012030 ... ... ... ... 3496 chrX 2328562 2328572 3497 chrX 2328572 2328582 3498 chrX 2328582 2328592 3499 chrX 2328592 2328602 3500 chrX 2328602 2328605 [3501 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpc5ab52fj/f1.bed) bedtools_df Chromosome Start End 0 chr1 916989 916999 1 chr1 916999 917009 2 chr1 917009 917019 3 chr1 917019 917029 4 chr1 917029 917039 ... ... ... ... 5818 chr22 7455080 7455090 5819 chr22 7455090 7455100 5820 chr22 7455100 7455110 5821 chr22 7455110 7455120 5822 chr22 7455120 7455126 [5823 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp76rllb56/f1.bed) bedtools_df Chromosome Start End 0 chr1 2 12 1 chr1 12 22 2 chr1 22 32 3 chr1 32 42 4 chr1 42 52 ... ... ... ... 5740 chrM 6498045 6498055 5741 chrM 6498055 6498065 5742 chrM 6498065 6498075 5743 chrM 6498075 6498085 5744 chrM 6498085 6498088 [5745 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp9pv6ef34/f1.bed) bedtools_df Chromosome Start End 0 chr1 555027 555037 1 chr1 555037 555047 2 chr1 555047 555057 3 chr1 555057 555067 4 chr1 555067 555077 ... ... ... ... 3943 chr7 10009949 10009959 3944 chr7 10009959 10009969 3945 chr7 10009969 10009979 3946 chr7 10009979 10009989 3947 chr7 10009989 10009999 [3948 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpen9ygdt8/f1.bed) bedtools_df Chromosome Start End 0 chr1 1989926 1989936 1 chr1 1989936 1989946 2 chr1 1989946 1989956 3 chr1 1989956 1989966 4 chr1 1989966 1989976 ... ... ... ... 3015 chrY 3878947 3878957 3016 chrY 3878957 3878967 3017 chrY 3878967 3878977 3018 chrY 3878977 3878987 3019 chrY 3878987 3878997 [3020 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp1p8oq69i/f1.bed) bedtools_df Chromosome Start End 0 chr1 3643641 3643651 1 chr1 3643651 3643661 2 chr1 3643661 3643671 3 chr1 3643671 3643681 4 chr1 3643681 3643691 ... ... ... ... 3878 chrY 3647541 3647551 3879 chrY 3647551 3647561 3880 chrY 3647561 3647571 3881 chrY 3647571 3647581 3882 chrY 3647581 3647583 [3883 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqjyzq4mr/f1.bed) bedtools_df Chromosome Start End 0 chr1 2269753 2269763 1 chr1 2269763 2269773 2 chr1 2269773 2269783 3 chr1 2269783 2269793 4 chr1 2269793 2269803 .. ... ... ... 274 chr1 2272493 2272503 275 chr1 2272503 2272513 276 chr1 2272513 2272523 277 chr1 2272523 2272533 278 chr1 2272533 2272542 [279 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpy2onuv8p/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 ... ... ... ... 4361 chr22 7107616 7107626 4362 chr22 7107626 7107636 4363 chr22 7107636 7107646 4364 chr22 7107646 7107656 4365 chr22 7107656 7107663 [4366 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv0z9_2av/f1.bed) bedtools_df Chromosome Start End 0 chr15 2155343 2155353 1 chr15 2155353 2155363 2 chr15 2155363 2155373 3 chr15 2155373 2155383 4 chr15 2155383 2155393 .. ... ... ... 793 chr15 2163273 2163283 794 chr15 2163283 2163293 795 chr15 2163293 2163303 796 chr15 2163303 2163313 797 chr15 2163313 2163315 [798 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpnak8a2va/f1.bed) bedtools_df Chromosome Start End 0 chr1 130925 130935 1 chr1 130935 130945 2 chr1 130945 130955 3 chr1 130955 130965 4 chr1 130965 130975 ... ... ... ... 5463 chrY 81261 81271 5464 chrY 81271 81281 5465 chrY 81281 81291 5466 chrY 81291 81301 5467 chrY 81301 81305 [5468 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpm_1pfir8/f1.bed) bedtools_df Chromosome Start End 0 chr1 1912953 1912963 1 chr1 1912963 1912973 2 chr1 1912973 1912983 3 chr1 1912983 1912993 4 chr1 1912993 1913003 ... ... ... ... 9118 chr6 4852286 4852296 9119 chr6 4852296 4852306 9120 chr6 4852306 4852316 9121 chr6 4852316 4852326 9122 chr6 4852326 4852335 [9123 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpdtgt5t0h/f1.bed) bedtools_df Chromosome Start End 0 chr1 8382766 8382776 1 chr1 8382776 8382786 2 chr1 8382786 8382796 3 chr1 8382796 8382806 4 chr1 8382806 8382816 .. ... ... ... 659 chr1 8389356 8389366 660 chr1 8389366 8389376 661 chr1 8389376 8389386 662 chr1 8389386 8389396 663 chr1 8389396 8389400 [664 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplnf24ove/f1.bed) bedtools_df Chromosome Start End 0 chr1 4077440 4077450 1 chr1 4077450 4077460 2 chr1 4077460 4077470 3 chr1 4077470 4077480 4 chr1 4077480 4077490 ... ... ... ... 3950 chrM 5254124 5254134 3951 chrM 5254134 5254144 3952 chrM 5254144 5254154 3953 chrM 5254154 5254164 3954 chrM 5254164 5254170 [3955 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxrxd6zfx/f1.bed) bedtools_df Chromosome Start End 0 chr1 1645136 1645146 1 chr1 1645146 1645156 2 chr1 1645156 1645166 3 chr1 1645166 1645176 4 chr1 1645176 1645186 ... ... ... ... 6452 chr9 1651586 1651596 6453 chr9 1651596 1651606 6454 chr9 1651606 1651616 6455 chr9 1651616 1651626 6456 chr9 1651626 1651635 [6457 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpge9yzem_/f1.bed) bedtools_df Chromosome Start End 0 chr5 997944 997954 1 chr5 997954 997964 2 chr5 997964 997974 3 chr5 997974 997984 4 chr5 997984 997994 .. ... ... ... 646 chr5 1004404 1004414 647 chr5 1004414 1004424 648 chr5 1004424 1004434 649 chr5 1004434 1004444 650 chr5 1004444 1004452 [651 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpiseaa_pu/f1.bed) bedtools_df Chromosome Start End 0 chr1 125392 125402 1 chr1 125402 125412 2 chr1 125412 125422 3 chr1 125422 125432 4 chr1 125432 125442 ... ... ... ... 4921 chr9 8968151 8968161 4922 chr9 8968161 8968171 4923 chr9 8968171 8968181 4924 chr9 8968181 8968191 4925 chr9 8968191 8968199 [4926 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp61vatm21/f1.bed) bedtools_df Chromosome Start End 0 chr1 5289473 5289483 1 chr1 5289483 5289493 2 chr1 5289493 5289503 3 chr1 5289503 5289513 4 chr1 5289513 5289523 ... ... ... ... 1338 chr6 7744453 7744463 1339 chr6 7744463 7744473 1340 chr6 7744473 7744483 1341 chr6 7744483 7744493 1342 chr6 7744493 7744494 [1343 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpk42vzxo2/f1.bed) bedtools_df Chromosome Start End 0 chr1 5521490 5521500 1 chr1 5521500 5521510 2 chr1 5521510 5521520 3 chr1 5521520 5521530 4 chr1 5521530 5521540 ... ... ... ... 2185 chr5 4505724 4505734 2186 chr5 4505734 4505744 2187 chr5 4505744 4505754 2188 chr5 4505754 4505764 2189 chr5 4505764 4505767 [2190 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_r93dc93/f1.bed) bedtools_df Chromosome Start End 0 chr1 719229 719239 1 chr1 719239 719249 2 chr1 719249 719259 3 chr1 719259 719269 4 chr1 719269 719279 ... ... ... ... 4807 chr6 8078845 8078855 4808 chr6 8078855 8078865 4809 chr6 8078865 8078875 4810 chr6 8078875 8078885 4811 chr6 8078885 8078887 [4812 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp78v_wum_/f1.bed) bedtools_df Chromosome Start End 0 chr1 1104466 1104476 1 chr1 1104476 1104486 2 chr1 1104486 1104496 3 chr1 1104496 1104506 4 chr1 1104506 1104516 ... ... ... ... 1073 chr7 5882320 5882330 1074 chr7 5882330 5882340 1075 chr7 5882340 5882350 1076 chr7 5882350 5882360 1077 chr7 5882360 5882362 [1078 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp98zvz794/f1.bed) bedtools_df Chromosome Start End 0 chr1 6875959 6875969 1 chr1 6875969 6875979 2 chr1 6875979 6875989 3 chr1 6875989 6875999 4 chr1 6875999 6876009 .. ... ... ... 194 chr1 6877899 6877909 195 chr1 6877909 6877919 196 chr1 6877919 6877929 197 chr1 6877929 6877939 198 chr1 6877939 6877940 [199 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp85t55qtg/f1.bed) bedtools_df Chromosome Start End 0 chr16 6639122 6639132 1 chr16 6639132 6639142 2 chr16 6639142 6639152 3 chr16 6639152 6639162 4 chr16 6639162 6639172 .. ... ... ... 767 chr16 6646792 6646802 768 chr16 6646802 6646812 769 chr16 6646812 6646822 770 chr16 6646822 6646824 771 chr9 1790816 1790818 [772 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp5z7t2xcq/f1.bed) bedtools_df Chromosome Start End 0 chr1 2777106 2777116 1 chr1 2777116 2777126 2 chr1 2777126 2777136 3 chr1 2777136 2777146 4 chr1 2777146 2777156 .. ... ... ... 912 chr4 7954783 7954793 913 chr4 7954793 7954803 914 chr4 7954803 7954813 915 chr4 7954813 7954823 916 chr4 7954823 7954826 [917 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp68cousub/f1.bed) bedtools_df Chromosome Start End 0 chr1 1481453 1481463 1 chr1 1481463 1481473 2 chr1 1481473 1481483 3 chr1 1481483 1481493 4 chr1 1481493 1481503 ... ... ... ... 2914 chrY 8464854 8464864 2915 chrY 8464864 8464874 2916 chrY 8464874 8464884 2917 chrY 8464884 8464894 2918 chrY 8464894 8464899 [2919 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpefmtj_ul/f1.bed) bedtools_df Chromosome Start End 0 chr1 6422064 6422074 1 chr1 6422074 6422084 2 chr1 6422084 6422094 3 chr1 6422094 6422104 4 chr1 6422104 6422114 ... ... ... ... 2804 chr5 4416536 4416546 2805 chr5 4416546 4416556 2806 chr5 4416556 4416566 2807 chr5 4416566 4416576 2808 chr5 4416576 4416585 [2809 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplbya0vxc/f1.bed) bedtools_df Chromosome Start End 0 chr1 3535596 3535606 1 chr1 3535606 3535616 2 chr1 3535616 3535626 3 chr1 3535626 3535636 4 chr1 3535636 3535646 .. ... ... ... 952 chr1 3545116 3545126 953 chr1 3545126 3545136 954 chr1 3545136 3545146 955 chr1 3545146 3545156 956 chr1 3545156 3545161 [957 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpgkyftinj/f1.bed) bedtools_df Chromosome Start End 0 chr1 2006356 2006366 1 chr1 2006366 2006376 2 chr1 2006376 2006386 3 chr1 2006386 2006396 4 chr1 2006396 2006406 ... ... ... ... 1564 chr17 10005180 10005190 1565 chr17 10005190 10005200 1566 chr17 10005200 10005210 1567 chr17 10005210 10005220 1568 chr17 10005220 10005229 [1569 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplbkc6n76/f1.bed) bedtools_df Chromosome Start End 0 chr1 8849505 8849515 1 chr1 8849515 8849525 2 chr1 8849525 8849535 3 chr1 8849535 8849545 4 chr1 8849545 8849555 .. ... ... ... 629 chr1 8855795 8855805 630 chr1 8855805 8855815 631 chr1 8855815 8855825 632 chr1 8855825 8855835 633 chr1 8855835 8855839 [634 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpd5bbco3q/f1.bed) bedtools_df Chromosome Start End 0 chr1 4592231 4592241 1 chr1 4592241 4592251 2 chr1 4592251 4592261 3 chr1 4592261 4592271 4 chr1 4592271 4592281 ... ... ... ... 5336 chrX 9543036 9543046 5337 chrX 9543046 9543056 5338 chrX 9543056 9543066 5339 chrX 9543066 9543076 5340 chrX 9543076 9543080 [5341 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3w4f3gak/f1.bed) bedtools_df Chromosome Start End 0 chr1 83697 83707 1 chr1 83707 83717 2 chr1 83717 83727 3 chr1 83727 83737 4 chr1 83737 83747 ... ... ... ... 3947 chrM 558247 558257 3948 chrM 558257 558267 3949 chrM 558267 558277 3950 chrM 558277 558287 3951 chrM 558287 558290 [3952 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpafno4s4v/f1.bed) bedtools_df Chromosome Start End 0 chr1 1605475 1605485 1 chr1 1605485 1605495 2 chr1 1605495 1605505 3 chr1 1605505 1605515 4 chr1 1605515 1605525 ... ... ... ... 2089 chr4 1553307 1553317 2090 chr4 1553317 1553327 2091 chr4 1553327 1553337 2092 chr4 1553337 1553347 2093 chr4 1553347 1553348 [2094 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpmot4ayqt/f1.bed) bedtools_df Chromosome Start End 0 chr1 7666882 7666892 1 chr1 7666892 7666902 2 chr1 7666902 7666912 3 chr1 7666912 7666922 4 chr1 7666922 7666932 ... ... ... ... 5148 chrY 7675842 7675852 5149 chrY 7675852 7675862 5150 chrY 7675862 7675872 5151 chrY 7675872 7675882 5152 chrY 7675882 7675885 [5153 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpa6oqc5ri/f1.bed) bedtools_df Chromosome Start End 0 chr1 1719876 1719886 1 chr1 1719886 1719896 2 chr1 1719896 1719906 3 chr1 1719906 1719916 4 chr1 1719916 1719926 ... ... ... ... 5860 chrM 6637590 6637600 5861 chrM 6637600 6637610 5862 chrM 6637610 6637620 5863 chrM 6637620 6637630 5864 chrM 6637630 6637632 [5865 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8r7c5y1_/f1.bed) bedtools_df Chromosome Start End 0 chr1 2094673 2094683 1 chr1 2094683 2094693 2 chr1 2094693 2094703 3 chr1 2094703 2094713 4 chr1 2094713 2094723 ... ... ... ... 1635 chr20 2096313 2096323 1636 chr20 2096323 2096333 1637 chr20 2096333 2096343 1638 chr20 2096343 2096353 1639 chr20 2096353 2096363 [1640 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp1z383cia/f1.bed) bedtools_df Chromosome Start End 0 chr22 5255799 5255801 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmps__aco7e/f1.bed) bedtools_df Chromosome Start End 0 chr1 3021289 3021299 1 chr1 3021299 3021309 2 chr1 3021309 3021319 3 chr1 3021319 3021329 4 chr1 3021329 3021339 ... ... ... ... 4216 chr3 9404601 9404611 4217 chr3 9404611 9404621 4218 chr3 9404621 9404631 4219 chr3 9404631 9404641 4220 chr3 9404641 9404646 [4221 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpj3tz4a39/f1.bed) bedtools_df Chromosome Start End 0 chr1 26421 26431 1 chr1 26431 26441 2 chr1 26441 26451 3 chr1 26451 26461 4 chr1 26461 26471 ... ... ... ... 3664 chr8 8851393 8851403 3665 chr8 8851403 8851413 3666 chr8 8851413 8851423 3667 chr8 8851423 8851433 3668 chr8 8851433 8851435 [3669 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpcx03q9nv/f1.bed) bedtools_df Chromosome Start End 0 chr1 861808 861818 1 chr1 861818 861828 2 chr1 861828 861838 3 chr1 861838 861848 4 chr1 861848 861858 ... ... ... ... 6589 chrM 869558 869568 6590 chrM 869568 869578 6591 chrM 869578 869588 6592 chrM 869588 869598 6593 chrM 869598 869602 [6594 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmppljz2op6/f1.bed) bedtools_df Chromosome Start End 0 chr1 2116362 2116372 1 chr1 2116372 2116382 2 chr1 2116382 2116392 3 chr1 2116392 2116402 4 chr1 2116402 2116412 ... ... ... ... 2633 chr3 1096448 1096458 2634 chr3 1096458 1096468 2635 chr3 1096468 1096478 2636 chr3 1096478 1096488 2637 chr3 1096488 1096491 [2638 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpx5myu5gm/f1.bed) bedtools_df Chromosome Start End 0 chr1 9524073 9524083 1 chr1 9524083 9524093 2 chr1 9524093 9524103 3 chr1 9524103 9524113 4 chr1 9524113 9524123 ... ... ... ... 4255 chr15 10001460 10001470 4256 chr15 10001470 10001480 4257 chr15 10001480 10001490 4258 chr15 10001490 10001500 4259 chr15 10001500 10001506 [4260 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp65z7evy_/f1.bed) bedtools_df Chromosome Start End 0 chr1 4511655 4511657 1 chr1 4573318 4573328 2 chr1 4573328 4573338 3 chr1 4573338 4573348 4 chr1 4573348 4573358 ... ... ... ... 5635 chrY 4547245 4547255 5636 chrY 4547255 4547265 5637 chrY 4547265 4547275 5638 chrY 4547275 4547285 5639 chrY 4547285 4547289 [5640 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpixp2l4z7/f1.bed) bedtools_df Chromosome Start End 0 chr1 4634715 4634725 1 chr1 4634725 4634735 2 chr1 4634735 4634745 3 chr1 4634745 4634755 4 chr1 4634755 4634765 ... ... ... ... 4708 chr21 5410622 5410632 4709 chr21 5410632 5410642 4710 chr21 5410642 5410652 4711 chr21 5410652 5410662 4712 chr21 5410662 5410666 [4713 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpfr7pxzo9/f1.bed) bedtools_df Chromosome Start End 0 chrX 5734223 5734233 1 chrX 5734233 5734243 2 chrX 5734243 5734253 3 chrX 5734253 5734263 4 chrX 5734263 5734273 .. ... ... ... 178 chrX 5736003 5736013 179 chrX 5736013 5736023 180 chrX 5736023 5736033 181 chrX 5736033 5736043 182 chrX 5736043 5736047 [183 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp9_j_u936/f1.bed) bedtools_df Chromosome Start End 0 chr1 2460582 2460592 1 chr1 2460592 2460602 2 chr1 2460602 2460612 3 chr1 2460612 2460622 4 chr1 2460622 2460632 ... ... ... ... 3986 chr18 2637091 2637101 3987 chr18 2637101 2637111 3988 chr18 2637111 2637121 3989 chr18 2637121 2637131 3990 chr18 2637131 2637138 [3991 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpeqpq3c1e/f1.bed) bedtools_df Chromosome Start End 0 chr1 2641177 2641187 1 chr1 2641187 2641197 2 chr1 2641197 2641207 3 chr1 2641207 2641217 4 chr1 2641217 2641227 ... ... ... ... 6562 chr22 9816712 9816722 6563 chr22 9816722 9816732 6564 chr22 9816732 9816742 6565 chr22 9816742 9816752 6566 chr22 9816752 9816755 [6567 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpq57vapc0/f1.bed) bedtools_df Chromosome Start End 0 chr1 2938178 2938188 1 chr1 2938188 2938198 2 chr1 2938198 2938208 3 chr1 2938208 2938218 4 chr1 2938218 2938228 ... ... ... ... 5128 chr7 6083643 6083653 5129 chr7 6083653 6083663 5130 chr7 6083663 6083673 5131 chr7 6083673 6083683 5132 chr7 6083683 6083685 [5133 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwnkq2_pp/f1.bed) bedtools_df Chromosome Start End 0 chr1 6156593 6156603 1 chr1 6156603 6156613 2 chr1 6156613 6156623 3 chr1 6156623 6156633 4 chr1 6156633 6156643 ... ... ... ... 1647 chr8 5328176 5328186 1648 chr8 5328186 5328196 1649 chr8 5328196 5328206 1650 chr8 5328206 5328216 1651 chr8 5328216 5328226 [1652 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxrbl8f9r/f1.bed) bedtools_df Chromosome Start End 0 chr1 4380261 4380271 1 chr1 4380271 4380281 2 chr1 4380281 4380291 3 chr1 4380291 4380301 4 chr1 4380301 4380311 ... ... ... ... 1669 chr12 4383720 4383730 1670 chr12 4383730 4383740 1671 chr12 4383740 4383750 1672 chr12 4383750 4383760 1673 chr12 4383760 4383769 [1674 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxilomi91/f1.bed) bedtools_df Chromosome Start End 0 chr1 195009 195019 1 chr1 195019 195029 2 chr1 195029 195039 3 chr1 195039 195049 4 chr1 195049 195059 ... ... ... ... 2904 chrX 520008 520018 2905 chrX 520018 520028 2906 chrX 520028 520038 2907 chrX 520038 520048 2908 chrX 520048 520050 [2909 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpy074k6mi/f1.bed) bedtools_df Chromosome Start End 0 chr10 2177604 2177614 1 chr10 2177614 2177624 2 chr10 2177624 2177634 3 chr10 2177634 2177644 4 chr10 2177644 2177654 .. ... ... ... 852 chr7 2523855 2523865 853 chr7 2523865 2523875 854 chr7 2523875 2523885 855 chr7 2523885 2523895 856 chr7 2523895 2523901 [857 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpk0ug5rj1/f1.bed) bedtools_df Chromosome Start End 0 chr1 3713862 3713872 1 chr1 3713872 3713882 2 chr1 3713882 3713892 3 chr1 3713892 3713902 4 chr1 3713902 3713912 .. ... ... ... 807 chr1 3721932 3721942 808 chr1 3721942 3721952 809 chr1 3721952 3721962 810 chr1 3721962 3721972 811 chr1 3721972 3721977 [812 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp637gaszq/f1.bed) bedtools_df Chromosome Start End 0 chr1 2562616 2562626 1 chr1 2562626 2562636 2 chr1 2562636 2562646 3 chr1 2562646 2562656 4 chr1 2562656 2562666 ... ... ... ... 4224 chr14 2031559 2031569 4225 chr14 2031569 2031579 4226 chr14 2031579 2031589 4227 chr14 2031589 2031599 4228 chr14 2031599 2031609 [4229 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwi0ssp0k/f1.bed) bedtools_df Chromosome Start End 0 chr1 1162983 1162984 1 chr1 2726296 2726306 2 chr1 2726306 2726316 3 chr1 2726316 2726326 4 chr1 2726326 2726336 ... ... ... ... 4506 chr8 7916434 7916444 4507 chr8 7916444 7916454 4508 chr8 7916454 7916464 4509 chr8 7916464 7916474 4510 chr8 7916474 7916476 [4511 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpz3shaodv/f1.bed) bedtools_df Chromosome Start End 0 chr1 1065787 1065797 1 chr1 1065797 1065807 2 chr1 1065807 1065817 3 chr1 1065817 1065827 4 chr1 1065827 1065837 ... ... ... ... 2634 chrY 9740862 9740872 2635 chrY 9740872 9740882 2636 chrY 9740882 9740892 2637 chrY 9740892 9740902 2638 chrY 9740902 9740907 [2639 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_6ec7m68/f1.bed) bedtools_df Chromosome Start End 0 chr1 5698087 5698097 1 chr1 5698097 5698107 2 chr1 5698107 5698117 3 chr1 5698117 5698127 4 chr1 5698127 5698137 ... ... ... ... 2409 chr15 9036379 9036389 2410 chr15 9036389 9036399 2411 chr15 9036399 9036409 2412 chr15 9036409 9036419 2413 chr15 9036419 9036426 [2414 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpaupdamet/f1.bed) bedtools_df Chromosome Start End 0 chr1 1010676 1010686 1 chr1 1010686 1010696 2 chr1 1010696 1010706 3 chr1 1010706 1010716 4 chr1 1010716 1010726 ... ... ... ... 5736 chr7 7123127 7123137 5737 chr7 7123137 7123147 5738 chr7 7123147 7123157 5739 chr7 7123157 7123167 5740 chr7 7123167 7123169 [5741 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpfr940xbf/f1.bed) bedtools_df Chromosome Start End 0 chr1 1925558 1925568 1 chr1 1925568 1925578 2 chr1 1925578 1925588 3 chr1 1925588 1925598 4 chr1 1925598 1925608 ... ... ... ... 3781 chr8 8568559 8568562 3782 chrX 5601837 5601847 3783 chrX 5601847 5601857 3784 chrX 5601857 5601867 3785 chrX 5601867 5601874 [3786 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpbqqzlq_4/f1.bed) bedtools_df Chromosome Start End 0 chr1 386199 386209 1 chr1 386209 386219 2 chr1 386219 386229 3 chr1 386229 386239 4 chr1 386239 386249 ... ... ... ... 5318 chr16 8631067 8631077 5319 chr16 8631077 8631087 5320 chr16 8631087 8631097 5321 chr16 8631097 8631107 5322 chr16 8631107 8631115 [5323 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8d2fgx66/f1.bed) bedtools_df Chromosome Start End 0 chr1 1056935 1056945 1 chr1 1056945 1056955 2 chr1 1056955 1056965 3 chr1 1056965 1056975 4 chr1 1056975 1056985 ... ... ... ... 2968 chr5 7717874 7717884 2969 chr5 7717884 7717894 2970 chr5 7717894 7717904 2971 chr5 7717904 7717914 2972 chr5 7717914 7717916 [2973 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwkd8bqxc/f1.bed) bedtools_df Chromosome Start End 0 chr1 776069 776079 1 chr1 776079 776089 2 chr1 776089 776099 3 chr1 776099 776109 4 chr1 776109 776119 ... ... ... ... 2877 chr5 1961038 1961048 2878 chr5 1961048 1961058 2879 chr5 1961058 1961068 2880 chr5 1961068 1961078 2881 chr5 1961078 1961086 [2882 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxh7vnkg4/f1.bed) bedtools_df Chromosome Start End 0 chr1 3760509 3760519 1 chr1 3760519 3760529 2 chr1 3760529 3760539 3 chr1 3760539 3760549 4 chr1 3760549 3760559 ... ... ... ... 6422 chr5 8213292 8213302 6423 chr5 8213302 8213312 6424 chr5 8213312 8213322 6425 chr5 8213322 8213332 6426 chr5 8213332 8213333 [6427 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpo8y_e9cb/f1.bed) bedtools_df Chromosome Start End 0 chr1 2680090 2680100 1 chr1 2680100 2680110 2 chr1 2680110 2680120 3 chr1 2680120 2680130 4 chr1 2680130 2680140 .. ... ... ... 377 chr1 2683860 2683870 378 chr1 2683870 2683880 379 chr1 2683880 2683890 380 chr1 2683890 2683900 381 chr1 2683900 2683909 [382 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp81oso72v/f1.bed) bedtools_df Chromosome Start End 0 chr8 6210457 6210467 1 chr8 6210467 6210477 2 chr8 6210477 6210487 3 chr8 6210487 6210497 4 chr8 6210497 6210507 .. ... ... ... 539 chr8 6215847 6215857 540 chr8 6215857 6215867 541 chr8 6215867 6215877 542 chr8 6215877 6215887 543 chr8 6215887 6215897 [544 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpx18lz2gq/f1.bed) bedtools_df Chromosome Start End 0 chr1 2 12 1 chr1 12 22 2 chr1 22 32 3 chr1 32 42 4 chr1 42 52 ... ... ... ... 1683 chrY 6531976 6531986 1684 chrY 6531986 6531996 1685 chrY 6531996 6532006 1686 chrY 6532006 6532016 1687 chrY 6532016 6532024 [1688 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_upvvsbu/f1.bed) bedtools_df Chromosome Start End 0 chr1 384889 384899 1 chr1 384899 384909 2 chr1 384909 384919 3 chr1 384919 384929 4 chr1 384929 384939 ... ... ... ... 1585 chr1 9067341 9067351 1586 chr1 9067351 9067361 1587 chr1 9067361 9067371 1588 chr1 9067371 9067381 1589 chr1 9067381 9067382 [1590 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpu3ocp_tq/f1.bed) bedtools_df Chromosome Start End 0 chr1 1385103 1385113 1 chr1 1385113 1385123 2 chr1 1385123 1385133 3 chr1 1385133 1385143 4 chr1 1385143 1385153 ... ... ... ... 3748 chr21 10000349 10000359 3749 chr21 10000359 10000369 3750 chr21 10000369 10000379 3751 chr21 10000379 10000389 3752 chr21 10000389 10000392 [3753 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpsvebp_1w/f1.bed) bedtools_df Chromosome Start End 0 chr1 2241555 2241565 1 chr1 2241565 2241575 2 chr1 2241575 2241585 3 chr1 2241585 2241587 4 chrX 7788951 7788961 .. ... ... ... 311 chrX 7792021 7792031 312 chrX 7792031 7792041 313 chrX 7792041 7792051 314 chrX 7792051 7792061 315 chrX 7792061 7792067 [316 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpfz9wk6qb/f1.bed) bedtools_df Chromosome Start End 0 chr1 1552650 1552660 1 chr1 1552660 1552670 2 chr1 1552670 1552680 3 chr1 1552680 1552690 4 chr1 1552690 1552700 ... ... ... ... 4390 chrX 268770 268780 4391 chrX 268780 268790 4392 chrX 268790 268800 4393 chrX 268800 268810 4394 chrX 268810 268811 [4395 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_ce4g8tl/f1.bed) bedtools_df Chromosome Start End 0 chr1 6452021 6452031 1 chr1 6452031 6452041 2 chr1 6452041 6452051 3 chr1 6452051 6452061 4 chr1 6452061 6452071 ... ... ... ... 2164 chr4 6778971 6778981 2165 chr4 6778981 6778991 2166 chr4 6778991 6779001 2167 chr4 6779001 6779011 2168 chr4 6779011 6779014 [2169 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp425twy9v/f1.bed) bedtools_df Chromosome Start End 0 chr1 217316 217326 1 chr1 217326 217336 2 chr1 217336 217346 3 chr1 217346 217356 4 chr1 217356 217366 ... ... ... ... 3453 chr16 729303 729313 3454 chr16 729313 729323 3455 chr16 729323 729333 3456 chr16 729333 729343 3457 chrY 1134727 1134728 [3458 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpj5hzwwpz/f1.bed) bedtools_df Chromosome Start End 0 chr1 780468 780478 1 chr1 780478 780488 2 chr1 780488 780498 3 chr1 780498 780508 4 chr1 780508 780518 ... ... ... ... 5068 chr17 5098643 5098653 5069 chr17 5098653 5098663 5070 chr17 5098663 5098673 5071 chr17 5098673 5098683 5072 chr17 5098683 5098693 [5073 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp5eyx6tuq/f1.bed) bedtools_df Chromosome Start End 0 chr1 1137074 1137084 1 chr1 1137084 1137094 2 chr1 1137094 1137104 3 chr1 1137104 1137114 4 chr1 1137114 1137124 ... ... ... ... 4382 chr1 9531403 9531413 4383 chr1 9531413 9531423 4384 chr1 9531423 9531433 4385 chr1 9531433 9531443 4386 chr1 9531443 9531445 [4387 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplbnupnj_/f1.bed) bedtools_df Chromosome Start End 0 chr1 2 12 1 chr1 12 22 2 chr1 22 32 3 chr1 32 42 4 chr1 42 52 ... ... ... ... 3789 chr2 6877854 6877864 3790 chr2 6877864 6877874 3791 chr2 6877874 6877884 3792 chr2 6877884 6877894 3793 chr2 6877894 6877901 [3794 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptb2j_dpu/f1.bed) bedtools_df Chromosome Start End 0 chr1 1124087 1124097 1 chr1 1124097 1124107 2 chr1 1124107 1124117 3 chr1 1124117 1124127 4 chr1 1124127 1124137 ... ... ... ... 5568 chr7 1184695 1184705 5569 chr7 1184705 1184715 5570 chr7 1184715 1184725 5571 chr7 1184725 1184735 5572 chr7 1184735 1184745 [5573 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_2iz496k/f1.bed) bedtools_df Chromosome Start End 0 chr1 3304233 3304243 1 chr1 3304243 3304253 2 chr1 3304253 3304263 3 chr1 3304263 3304273 4 chr1 3304273 3304283 ... ... ... ... 1956 chrX 7871898 7871908 1957 chrX 7871908 7871918 1958 chrX 7871918 7871928 1959 chrX 7871928 7871938 1960 chrX 7871938 7871947 [1961 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpu5yiwib0/f1.bed) bedtools_df Chromosome Start End 0 chr1 501493 501503 1 chr1 501503 501513 2 chr1 501513 501523 3 chr1 501523 501533 4 chr1 501533 501543 ... ... ... ... 5682 chr7 7719983 7719993 5683 chr7 7719993 7720003 5684 chr7 7720003 7720013 5685 chr7 7720013 7720023 5686 chr7 7720023 7720030 [5687 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpc2yfd3zu/f1.bed) bedtools_df Chromosome Start End 0 chr1 3469213 3469223 1 chr1 3469223 3469233 2 chr1 3469233 3469243 3 chr1 3469243 3469253 4 chr1 3469253 3469263 ... ... ... ... 4628 chrX 7510868 7510878 4629 chrX 7510878 7510888 4630 chrX 7510888 7510898 4631 chrX 7510898 7510908 4632 chrX 7510908 7510913 [4633 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplko903nf/f1.bed) bedtools_df Chromosome Start End 0 chr1 2561884 2561894 1 chr1 2561894 2561904 2 chr1 2561904 2561914 3 chr1 2561914 2561924 4 chr1 2561924 2561934 ... ... ... ... 2012 chrX 8035654 8035664 2013 chrX 8035664 8035674 2014 chrX 8035674 8035684 2015 chrX 8035684 8035694 2016 chrX 8035694 8035702 [2017 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8c17tnhr/f1.bed) bedtools_df Chromosome Start End 0 chr1 1500615 1500625 1 chr1 1500625 1500635 2 chr1 1500635 1500645 3 chr1 1500645 1500655 4 chr1 1500655 1500665 .. ... ... ... 327 chr1 1503885 1503895 328 chr1 1503895 1503905 329 chr1 1503905 1503915 330 chr1 1503915 1503919 331 chr5 1086360 1086362 [332 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpy8c1eaq_/f1.bed) bedtools_df Chromosome Start End 0 chr1 513173 513183 1 chr1 513183 513193 2 chr1 513193 513203 3 chr1 513203 513213 4 chr1 513213 513223 ... ... ... ... 2095 chr4 4161454 4161464 2096 chr4 4161464 4161474 2097 chr4 4161474 4161484 2098 chr4 4161484 4161494 2099 chr4 4161494 4161497 [2100 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpb5fwku9h/f1.bed) bedtools_df Chromosome Start End 0 chr3 1909637 1909647 1 chr3 1909647 1909657 2 chr3 1909657 1909667 3 chr3 1909667 1909677 4 chr3 1909677 1909687 .. ... ... ... 955 chr3 1919187 1919197 956 chr3 1919197 1919207 957 chr3 1919207 1919217 958 chr3 1919217 1919227 959 chr3 1919227 1919235 [960 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmps0i39nig/f1.bed) bedtools_df Chromosome Start End 0 chr4 2578996 2579006 1 chr4 2579006 2579016 2 chr4 2579016 2579026 3 chr4 2579026 2579036 4 chr4 2579036 2579046 .. ... ... ... 931 chr4 2588306 2588316 932 chr4 2588316 2588326 933 chr4 2588326 2588336 934 chr4 2588336 2588346 935 chr4 2588346 2588350 [936 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpcz8zgic7/f1.bed) bedtools_df Chromosome Start End 0 chr1 275809 275819 1 chr1 275819 275829 2 chr1 275829 275839 3 chr1 275839 275849 4 chr1 275849 275859 ... ... ... ... 2394 chrM 6212812 6212822 2395 chrM 6212822 6212832 2396 chrM 6212832 6212842 2397 chrM 6212842 6212852 2398 chrM 6212852 6212856 [2399 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpp4gbrdxr/f1.bed) bedtools_df Chromosome Start End 0 chr1 5951523 5951533 1 chr1 5951533 5951543 2 chr1 5951543 5951553 3 chr1 5951553 5951563 4 chr1 5951563 5951573 ... ... ... ... 6799 chr8 7939237 7939247 6800 chr8 7939247 7939257 6801 chr8 7939257 7939267 6802 chr8 7939267 7939277 6803 chr8 7939277 7939279 [6804 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2eobuz77/f1.bed) bedtools_df Chromosome Start End 0 chr1 6691030 6691040 1 chr1 6691040 6691050 2 chr1 6691050 6691060 3 chr1 6691060 6691070 4 chr1 6691070 6691080 ... ... ... ... 2336 chr22 6698000 6698010 2337 chr22 6698010 6698020 2338 chr22 6698020 6698030 2339 chr22 6698030 6698040 2340 chr22 6698040 6698047 [2341 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3q5fgc65/f1.bed) bedtools_df Chromosome Start End 0 chr1 4593340 4593350 1 chr1 4593350 4593360 2 chr1 4593360 4593370 3 chr1 4593370 4593380 4 chr1 4593380 4593390 ... ... ... ... 5841 chr17 7723028 7723038 5842 chr17 7723038 7723048 5843 chr17 7723048 7723058 5844 chr17 7723058 7723068 5845 chr17 7723068 7723070 [5846 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwfi0v7fh/f1.bed) bedtools_df Chromosome Start End 0 chr1 830757 830767 1 chr1 830767 830777 2 chr1 830777 830787 3 chr1 830787 830797 4 chr1 830797 830807 ... ... ... ... 3437 chr6 7521335 7521345 3438 chr6 7521345 7521355 3439 chr6 7521355 7521365 3440 chr6 7521365 7521375 3441 chr6 7521375 7521381 [3442 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpp3p_1xxh/f1.bed) bedtools_df Chromosome Start End 0 chr1 389139 389149 1 chr1 389149 389159 2 chr1 389159 389169 3 chr1 389169 389179 4 chr1 389179 389189 ... ... ... ... 3223 chr10 6469098 6469108 3224 chr10 6469108 6469118 3225 chr10 6469118 6469128 3226 chr10 6469128 6469129 3227 chr21 1 2 [3228 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4lhywes2/f1.bed) bedtools_df Chromosome Start End 0 chr13 1931219 1931229 1 chr13 1931229 1931239 2 chr13 1931239 1931249 3 chr13 1931249 1931259 4 chr13 1931259 1931269 ... ... ... ... 1002 chr8 4212258 4212268 1003 chr8 4212268 4212278 1004 chr8 4212278 4212288 1005 chr8 4212288 4212298 1006 chr8 4212298 4212300 [1007 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjrv28hq0/f1.bed) bedtools_df Chromosome Start End 0 chr1 2711118 2711128 1 chr1 2711128 2711138 2 chr1 2711138 2711148 3 chr1 2711148 2711158 4 chr1 2711158 2711168 ... ... ... ... 5974 chr12 342 352 5975 chr12 352 362 5976 chr12 362 372 5977 chr12 372 382 5978 chr12 382 383 [5979 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0i1tpaqn/f1.bed) bedtools_df Chromosome Start End 0 chr1 647147 647157 1 chr1 647157 647167 2 chr1 647167 647177 3 chr1 647177 647187 4 chr1 647187 647197 ... ... ... ... 1226 chr11 6385703 6385713 1227 chr11 6385713 6385723 1228 chr11 6385723 6385733 1229 chr11 6385733 6385743 1230 chr11 6385743 6385752 [1231 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmporkhgyd0/f1.bed) bedtools_df Chromosome Start End 0 chr1 8194859 8194869 1 chr1 8194869 8194879 2 chr1 8194879 8194889 3 chr1 8194889 8194899 4 chr1 8194899 8194909 ... ... ... ... 9271 chr15 1757193 1757203 9272 chr15 1757203 1757213 9273 chr15 1757213 1757223 9274 chr15 1757223 1757233 9275 chr15 1757233 1757234 [9276 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2shb2zz5/f1.bed) bedtools_df Chromosome Start End 0 chr1 196802 196812 1 chr1 196812 196822 2 chr1 196822 196832 3 chr1 196832 196842 4 chr1 196842 196852 ... ... ... ... 6100 chr1 9086988 9086998 6101 chr1 9086998 9087008 6102 chr1 9087008 9087018 6103 chr1 9087018 9087028 6104 chr1 9087028 9087031 [6105 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjwiwngll/f1.bed) bedtools_df Chromosome Start End 0 chr1 667357 667367 1 chr1 667367 667377 2 chr1 667377 667387 3 chr1 667387 667397 4 chr1 667397 667407 ... ... ... ... 4938 chrX 4254348 4254358 4939 chrX 4254358 4254368 4940 chrX 4254368 4254378 4941 chrX 4254378 4254388 4942 chrX 4254388 4254390 [4943 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpyfuk2ki8/f1.bed) bedtools_df Chromosome Start End 0 chr1 1659232 1659242 1 chr1 1659242 1659252 2 chr1 1659252 1659262 3 chr1 1659262 1659272 4 chr1 1659272 1659282 ... ... ... ... 5714 chr5 2145356 2145366 5715 chr5 2145366 2145376 5716 chr5 2145376 2145386 5717 chr5 2145386 2145396 5718 chr5 2145396 2145401 [5719 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpx69sr8m2/f1.bed) bedtools_df Chromosome Start End 0 chrY 42988 42998 1 chrY 42998 43008 2 chrY 43008 43018 3 chrY 43018 43028 4 chrY 43028 43038 ... ... ... ... 4388 chrY 7373997 7374007 4389 chrY 7374007 7374017 4390 chrY 7374017 7374027 4391 chrY 7374027 7374037 4392 chrY 7374037 7374047 [4393 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpak_cbi8f/f1.bed) bedtools_df Chromosome Start End 0 chr1 8943686 8943696 1 chr1 8943696 8943706 2 chr1 8943706 8943716 3 chr1 8943716 8943726 4 chr1 8943726 8943736 .. ... ... ... 875 chr19 8086518 8086528 876 chr19 8086528 8086538 877 chr19 8086538 8086548 878 chr19 8086548 8086558 879 chr19 8086558 8086564 [880 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwipagiz3/f1.bed) bedtools_df Chromosome Start End 0 chr13 7143256 7143266 1 chr13 7143266 7143276 2 chr13 7143276 7143286 3 chr13 7143286 7143296 4 chr13 7143296 7143306 ... ... ... ... 1076 chr18 7149026 7149036 1077 chr18 7149036 7149046 1078 chr18 7149046 7149056 1079 chr18 7149056 7149066 1080 chr18 7149066 7149069 [1081 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjf0w817i/f1.bed) bedtools_df Chromosome Start End 0 chr1 174780 174790 1 chr1 174790 174800 2 chr1 174800 174810 3 chr1 174810 174820 4 chr1 174820 174830 ... ... ... ... 4331 chr8 2462879 2462889 4332 chr8 2462889 2462899 4333 chr8 2462899 2462909 4334 chr8 2462909 2462919 4335 chr8 2462919 2462922 [4336 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpn3kwcn8l/f1.bed) bedtools_df Chromosome Start End 0 chr1 1447542 1447552 1 chr1 1447552 1447562 2 chr1 1447562 1447572 3 chr1 1447572 1447582 4 chr1 1447582 1447592 ... ... ... ... 4161 chrM 3468547 3468557 4162 chrM 3468557 3468567 4163 chrM 3468567 3468577 4164 chrM 3468577 3468587 4165 chrM 3468587 3468597 [4166 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6m4qn0vm/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 _________________________________ test_summary _________________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 @pytest.mark.bedtools > @settings( max_examples=max_examples, deadline=deadline, print_blob=True, suppress_health_check=HealthCheck.all()) tests/test_unary.py:311: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:322: in test_summary gr.summary() pyranges/pyranges.py:4475: in summary return _summary(self, to_stdout, return_df) pyranges/methods/summary.py:16: in _summary c = self.merge(strand=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_summary( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.99.9', b'AXicY2QAA0YGBAAAADIAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr13', 'chr13', 'chr13'], 'Start': [4068348, 1297440, 2308601, 8529828, 2596292, 7750862], 'End': [4072460, 1305959, 2311553, 8532541, 2599949, 7750909], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr7'], 'Start': [4068348, 394042, 3076, 4068348, 4068348], 'End': [4069891, 395839, 4875, 4069578, 4077827], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr7'], 'Start': [4068348, 394042, 3076, 4068348, 4068348], 'End': [4069891, 395839, 4875, 4069578, 4077827], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '+']} {'Chromosome': ['chr1', 'chr7', 'chr7', 'chr7'], 'Start': [393994, 656644, 656644, 656644], 'End': [395790, 658440, 658440, 658440], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '+', '+', '-']} {'Chromosome': ['chr1', 'chr7', 'chr7', 'chr7'], 'Start': [393994, 656644, 656644, 656644], 'End': [395790, 658440, 658440, 658440], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '+', '+', '-']} {'Chromosome': ['chr1', 'chr7', 'chr7', 'chr7'], 'Start': [393994, 656644, 656644, 656644], 'End': [395790, 658440, 658440, 658440], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr7', 'chr7', 'chr7'], 'Start': [393994, 656644, 656644, 656644], 'End': [395790, 658440, 658440, 658440], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [4154755], 'End': [4159139], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [4154755], 'End': [4159139], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr12', 'chr17', 'chr18', 'chr22'], 'Start': [8650735, 1369674, 4828105, 9999999, 6489489, 437935, 7116113, 5421554, 4328348, 5836110], 'End': [8658535, 1378471, 4831263, 10001546, 6496028, 446740, 7121957, 5424989, 4334142, 5839881], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr6', 'chr12', 'chr15', 'chr16'], 'Start': [8135676, 3346219, 6956271, 387448, 4833978], 'End': [8136710, 3355756, 6962265, 392991, 4836962], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr2', 'chr6', 'chrX'], 'Start': [7035343, 9098672, 8766582, 10000000, 7552711, 2093778], 'End': [7037893, 9107038, 8766583, 10003494, 7562568, 2100383], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr8', 'chr12', 'chr13', 'chr15', 'chr21'], 'Start': [4050055, 6037943, 3204962, 8869873, 4687191, 7576120, 8403438, 5544700, 8582476, 7559613], 'End': [4058873, 6042213, 3209634, 8874731, 4697143, 7580699, 8411247, 5553594, 8587517, 7567960], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '-', '+', '+', '+']} {'Chromosome': ['chr1', 'chr2', 'chr3', 'chr14'], 'Start': [8444842, 4872073, 6486947, 7149530], 'End': [8449273, 4876504, 6491378, 7150820], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr20'], 'Start': [8649422, 4549615, 4716109], 'End': [8655985, 4555346, 4718548], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'Start': [4857822, 10000000, 364051, 2084220, 9454049, 5796884, 990638, 5272759, 1501084, 4467608], 'End': [4867428, 10005285, 368235, 2088172, 9454120, 5806613, 990639, 5273938, 1511046, 4471731], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr3', 'chr8', 'chr10', 'chr20'], 'Start': [2773345, 9914940, 484944, 5898935, 2, 9728630, 1421133, 5176583, 6043324, 827836], 'End': [2778409, 9919627, 489631, 5903622, 448, 9735830, 1425820, 5184277, 6050101, 829776], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '+', '+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr8', 'chr15', 'chr17', 'chr20', 'chrX', 'chrY'], 'Start': [3167946, 5108459, 5066623, 3369334, 7375434, 8554790, 2382868, 2925156, 5304002, 9895992], 'End': [3168795, 5115965, 5066624, 3374172, 7376421, 8555864, 2385421, 2932282, 5310579, 9901093], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr16'], 'Start': [2247461, 5057948, 7598822], 'End': [2255890, 5062722, 7603596], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4973425, 6712189], 'End': [4982093, 6715020], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chrX'], 'Start': [3013761, 5639346], 'End': [3017955, 5642432], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr17', 'chrX'], 'Start': [8858371, 7212510, 3980989, 5987247, 8320573, 5509749, 7906561, 7991681], 'End': [8861770, 7220368, 3983604, 5994549, 8329482, 5515736, 7916038, 7998120], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '-', '+']} {'Chromosome': ['chr1'], 'Start': [9495796], 'End': [9497701], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr16'], 'Start': [1522090, 9941921, 7186420, 1395872, 4568643, 9643659], 'End': [1524344, 9950861, 7187458, 1403234, 4574288, 9648700], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr9', 'chrX'], 'Start': [2, 9755093, 6052477, 1170914], 'End': [5179, 9755694, 6060804, 1170958], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr7'], 'Start': [8001897, 7660913, 10000000], 'End': [8009767, 7667082, 10001613], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr4', 'chr13'], 'Start': [1411615, 1066295, 10000000, 9685478], 'End': [1416547, 1067118, 10009088, 9688097], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '+']} {'Chromosome': ['chr14'], 'Start': [3871999], 'End': [3873398], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr12', 'chr19', 'chr20'], 'Start': [9987186, 5532210, 1777703, 1777703, 1777703, 2245693, 10000000, 3416247, 8480325, 1777703], 'End': [9995798, 5535006, 1780225, 1780581, 1780354, 2254669, 10006211, 3423355, 8480941, 1785451], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr15'], 'Start': [3959639], 'End': [3962536], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr17', 'chr17', 'chr18', 'chr21'], 'Start': [1239938, 9673617, 5828792, 2701420, 1060814, 7168170, 2487031, 10000000, 3337549, 10000000], 'End': [1241037, 9680841, 5837417, 2706692, 1062288, 7171632, 2497030, 10009811, 3339196, 10001567], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr11', 'chr13', 'chr20', 'chrX', 'chrY'], 'Start': [7979856, 6436893, 5232780, 7984359, 8739076, 4747239, 7134454, 2390528, 1877249, 4582599], 'End': [7983297, 6437361, 5237600, 7988486, 8745983, 4749251, 7141793, 2394526, 1878811, 4589837], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chrX'], 'Start': [7984882, 824747, 9860205, 136828], 'End': [7984883, 829395, 9862121, 141476], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '-']} {'Chromosome': ['chr18'], 'Start': [4872409], 'End': [4877626], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [694168], 'End': [697613], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1'], 'Start': [9563599], 'End': [9563727], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1'], 'Start': [7559552], 'End': [7565336], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1'], 'Start': [5459976, 9203454, 6186932, 6131792], 'End': [5461472, 9205012, 6188470, 6141532], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '-']} {'Chromosome': ['chr1'], 'Start': [4760582], 'End': [4767476], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1'], 'Start': [3260991], 'End': [3261332], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr5', 'chr8', 'chr16'], 'Start': [9937253, 1, 616889, 1518758, 4116879], 'End': [9943259, 3517, 619255, 1528567, 4119002], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '-', '+', '+', '+']} {'Chromosome': ['chr1', 'chr11', 'chr22', 'chr22', 'chr22', 'chr22', 'chr22', 'chr22', 'chr22', 'chr22'], 'Start': [717161, 6403938, 305706, 717161, 3767692, 2584013, 717161, 4126139, 717161, 9818245], 'End': [727161, 6413938, 315706, 727161, 3777692, 2594013, 727161, 4136139, 727161, 9828245], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '+', '+', '+', '+', '+', '-', '-', '-']} {'Chromosome': ['chr11', 'chr16'], 'Start': [5949272, 2801331], 'End': [5954640, 2801521], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr11'], 'Start': [4793904, 3707857, 130309, 303190], 'End': [4803904, 3716203, 133442, 312328], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [7333064], 'End': [7333614], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr8', 'chr13', 'chr13', 'chr17', 'chrY'], 'Start': [2809632, 4330280, 8227160, 2893141, 8958860, 2180601, 4948065, 5191193, 6514605, 9506439], 'End': [2812666, 4337944, 8230824, 2903141, 8967872, 2189525, 4955402, 5199246, 6520235, 9515093], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [9449757, 5392485], 'End': [9458748, 5401476], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr8', 'chr19', 'chr21', 'chr21'], 'Start': [1316355, 5135715, 306935, 5570277, 5310958, 610909, 7514482], 'End': [1325426, 5144341, 309040, 5573070, 5313599, 618697, 7521445], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '+', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr12', 'chr17', 'chr17', 'chr17', 'chrX'], 'Start': [134560, 2367379, 8889916, 6633122, 1, 4490176, 4490176, 2737841, 10000000, 4490176], 'End': [134918, 2371567, 8890282, 6635904, 9594, 4492177, 4492009, 2744438, 10005574, 4498791], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr2', 'chr3', 'chr9', 'chr15', 'chr15', 'chr22', 'chrM'], 'Start': [6821400, 4383157, 517103, 4383157, 4383157, 8339326, 7654653, 4383157, 1347386, 4383157], 'End': [6821509, 4385870, 519620, 4388017, 4385870, 8342039, 7657366, 4393156, 1356872, 4391343], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr9', 'chr11'], 'Start': [3126126, 1403857, 5000453], 'End': [3134351, 1404085, 5010032], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr10', 'chr14', 'chr22', 'chr22', 'chrX'], 'Start': [4546846, 1, 7539645, 917522, 1, 1, 1400101, 2795201, 1, 1], 'End': [4556092, 6477, 7548137, 917940, 344, 6580, 1402544, 2798268, 695, 3868], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '+', '+', '+', '-']} {'Chromosome': ['chr1'], 'Start': [3822902], 'End': [3829823], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr13'], 'Start': [8284750, 2338534], 'End': [8289609, 2345064], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr15', 'chr21'], 'Start': [5664188, 6865362], 'End': [5672238, 6871921], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1'], 'Start': [3298542], 'End': [3301474], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr4', 'chr5', 'chr11', 'chr15'], 'Start': [5250488, 9462551, 8931601, 8884160, 9816977, 8000527], 'End': [5254950, 9470458, 8936113, 8888184, 9818721, 8006705], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'Start': [9226597, 6585375, 1, 7496185, 331343, 5687029, 8863884, 4051475], 'End': [9234901, 6594969, 9595, 7496632, 338195, 5696623, 8866506, 4061069], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr10', 'chr17', 'chr19'], 'Start': [4985965, 9683480, 10000000, 1469404, 10000000, 10000000], 'End': [4990427, 9687942, 10004462, 1473781, 10004462, 10005534], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chrX'], 'Start': [3306900, 8691033, 5838193, 2697656], 'End': [3312289, 8696014, 5838504, 2697950], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr14', 'chr14', 'chr14', 'chr22'], 'Start': [312403, 5749827, 8903569, 1378441, 6756490, 8327337], 'End': [314972, 5755727, 8912248, 1380588, 6756883, 8335852], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '+', '-', '-', '-']} {'Chromosome': ['chr7'], 'Start': [567094], 'End': [577093], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr6'], 'Start': [121177, 6845317], 'End': [127843, 6851983], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr8', 'chr15', 'chr15', 'chr15', 'chr16'], 'Start': [1, 4527513, 1796125, 1, 6518340, 8161441, 7278700, 4527513, 7223632, 5622297], 'End': [459, 4537325, 1805115, 2, 6522916, 8169227, 7288195, 4527936, 7230839, 5623427], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '+', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr3', 'chr7', 'chr11', 'chrX'], 'Start': [2644118, 666380, 4392368, 6338286, 7955382, 8073470], 'End': [2651135, 670759, 4402016, 6344868, 7963145, 8081008], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '+', '-', '-', '+']} {'Chromosome': ['chr1'], 'Start': [2715775], 'End': [2717997], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr9', 'chr13', 'chr16', 'chr18', 'chr19', 'chr21'], 'Start': [5633436, 5633436, 4339146, 3046417, 5729853, 1, 2324622, 5633436, 114479, 8170496], 'End': [5642072, 5639672, 4343635, 3055726, 5734214, 3000, 2325307, 5634953, 118015, 8178225], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '+', '-', '-', '-', '+', '-']} {'Chromosome': ['chr1'], 'Start': [4199607], 'End': [4203701], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr12', 'chr12', 'chr12', 'chr12', 'chr12', 'chr12', 'chr12'], 'Start': [2410191, 2441847, 5405820, 8979937, 3058282, 4678337, 1469975], 'End': [2412523, 2445911, 5407239, 8986906, 3063127, 4683336, 1479752], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr8', 'chr10', 'chr13', 'chr19', 'chr22'], 'Start': [4864642, 6595348, 5201774, 3925961, 3999418, 7596107, 9125052, 2297389, 507143, 6143964], 'End': [4873435, 6599311, 5209801, 3931690, 4002712, 7599033, 9134014, 2301962, 512671, 6148562], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr14', 'chr17'], 'Start': [9790396, 9999999, 7396948, 9229593, 3400029, 1578137], 'End': [9796290, 10001271, 7406107, 9230553, 3409188, 1587296], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr14', 'chr14'], 'Start': [4077244, 4077244, 4077244, 4077244, 4077244], 'End': [4086418, 4077553, 4085535, 4079531, 4081897], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr5', 'chr5', 'chr5', 'chr5', 'chr5', 'chr5', 'chrX'], 'Start': [1222375, 1657633, 8844233, 8844233, 7591549, 8844233, 4539385, 6606765, 8844233, 4886005], 'End': [1230582, 1658640, 8850581, 8848575, 7592133, 8844942, 4541371, 6616258, 8848980, 4886452], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '+', '+', '+', '+', '+', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4', 'chr8', 'chr21', 'chrX', 'chrX'], 'Start': [8024714, 6050257, 9085726, 8662729, 9815866, 3007651, 1340738, 5819597, 36081, 1], 'End': [8032144, 6050318, 9091737, 8664514, 9817900, 3010491, 1350222, 5825608, 43465, 3439], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-', '+', '+', '-', '-']} {'Chromosome': ['chr3', 'chr13', 'chr19', 'chr19'], 'Start': [249776, 7728572, 3494884, 249776], 'End': [255944, 7734999, 3504696, 257893], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr8', 'chrY'], 'Start': [7257842, 2335587, 377077, 1508462], 'End': [7258710, 2339507, 383441, 1511464], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '+']} {'Chromosome': ['chr1'], 'Start': [4760049], 'End': [4766323], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr10', 'chr10', 'chr16', 'chr21'], 'Start': [4369176, 6601442, 7735845, 7486816, 9826660, 8552476], 'End': [4378049, 6606287, 7745188, 7491195, 9830742, 8554486], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr2', 'chrM'], 'Start': [699152, 2724507, 9570925, 8887203, 3648197], 'End': [704651, 2726122, 9576424, 8892702, 3651115], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr7', 'chr17', 'chrX'], 'Start': [7329653, 5905454, 3851633, 6317325, 4565169, 2958239, 6780972, 9088357, 3042057, 3585260], 'End': [7337338, 5912109, 3859853, 6318128, 4574628, 2967922, 6781721, 9090210, 3051740, 3588317], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr18', 'chrM'], 'Start': [256244, 256244, 6967493, 10000000, 1258522, 8633826], 'End': [257107, 264927, 6973439, 10000001, 1260107, 8638351], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1'], 'Start': [3497960, 1125500, 5105883, 5823089], 'End': [3507153, 1130643, 5109292, 5832137], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr17', 'chr17', 'chr17'], 'Start': [6377728, 7270060, 7641930, 1302729, 5685146], 'End': [6380084, 7278798, 7650618, 1311467, 5686118], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-']} {'Chromosome': ['chr10'], 'Start': [3845140], 'End': [3852880], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr10'], 'Start': [10000000, 5048880, 9429536, 7242821, 4773030, 8183826], 'End': [10005888, 5051053, 9430044, 7252104, 4775234, 8185608], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [4802284], 'End': [4811327], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr3', 'chr4', 'chr12', 'chr18', 'chr22', 'chrX', 'chrY'], 'Start': [7901595, 1862788, 3844509, 1334307, 1, 3816132, 1885335, 2178261, 6203499], 'End': [7902354, 1869935, 3847373, 1342414, 5551, 3816495, 1888126, 2181062, 6203500], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '+', '-', '+', '-', '-']} {'Chromosome': ['chr14', 'chr14'], 'Start': [4404561, 8631272], 'End': [4411447, 8631434], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chrM', 'chrM', 'chrX'], 'Start': [7765269, 2830236, 7162391, 5035707, 7438794, 7520825, 1189130, 6974166], 'End': [7771639, 2832967, 7167191, 5037462, 7440736, 7522580, 1190885, 6976638], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '-', '-']} {'Chromosome': ['chr1'], 'Start': [10000000], 'End': [10001021], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [2809974, 2809974], 'End': [2811930, 2815682], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr3', 'chr11', 'chr15', 'chr16'], 'Start': [4518352, 726887, 452100, 6840679, 2398519, 6677776, 7454553, 3193461], 'End': [4519051, 733769, 454921, 6850365, 2403438, 6684681, 7462845, 3203163], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr13', 'chr21'], 'Start': [5946887, 2743085, 9126348, 6449887, 8341602, 9655821, 4847519, 9009815, 8668222, 3304505], 'End': [5948399, 2744597, 9130240, 6451730, 8343114, 9657333, 4855059, 9017267, 8669734, 3304506], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chrX'], 'Start': [4422177, 5481110, 3509123, 8932073, 8599928, 9263219, 6904744, 8398687], 'End': [4428203, 5488631, 3518617, 8936649, 8604742, 9267938, 6911880, 8408670], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr16'], 'Start': [8900684, 412169, 1026710, 5064725], 'End': [8900685, 421780, 1032110, 5068463], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'Start': [1802176, 1802176, 1802176, 1802176, 1802176, 1802176, 6640732, 2865266], 'End': [1807033, 1805111, 1806454, 1805111, 1805296, 1802785, 6643667, 2866208], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '-', '-', '-']} {'Chromosome': ['chr3'], 'Start': [8520288], 'End': [8526127], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr10', 'chr12'], 'Start': [5621317, 8671672], 'End': [5628339, 8674008], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr4', 'chr6'], 'Start': [4885729, 1694072, 3264267, 7080660, 4807657, 205312, 9757427, 7807752], 'End': [4894939, 1700714, 3273059, 7090660, 4816492, 214009, 9766672, 7812810], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1'], 'Start': [9720589], 'End': [9720591], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr9', 'chrM'], 'Start': [1858515, 4751854, 6298803, 3592158, 7459191, 5285576], 'End': [1861020, 4758403, 6305499, 3592278, 7469110, 5287670], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '+', '+']} {'Chromosome': ['chr1', 'chr16', 'chr17'], 'Start': [8477008, 9237266, 9649943], 'End': [8478955, 9241769, 9650831], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr18', 'chrM'], 'Start': [2728973, 1314994, 4233219, 9169300, 683078], 'End': [2735737, 1315305, 4240200, 9170021, 691299], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [3202311, 702876], 'End': [3210040, 710384], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr11', 'chr12'], 'Start': [10000000, 3862710, 2, 500238, 3467922], 'End': [10007563, 3865136, 3, 501384, 3468681], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr2'], 'Start': [6489242, 9622739], 'End': [6492181, 9629957], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr7', 'chr13', 'chr16', 'chr18'], 'Start': [8047354, 1493321, 8130427, 1493321], 'End': [8052046, 1502261, 8130813, 1498517], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr10', 'chr10', 'chr14', 'chr15', 'chr19'], 'Start': [1, 6338722, 3481581, 9047203, 1326428, 620990, 9241410, 2992880, 3665600, 5829151], 'End': [7444, 6342547, 3485449, 9052616, 1333444, 626451, 9251409, 3001782, 3671687, 5829152], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '+', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr9'], 'Start': [2758898, 8379102, 7606612], 'End': [2765432, 8385636, 7613146], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '-']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} _________________________________ test_windows _________________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 def test_windows(): f1 = pr.data.f1() print(f1) > result = f1.tile(2) tests/windows/test_windows.py:25: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/pyranges.py:4649: in tile df = pyrange_apply_single(_tiles, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:40: in _tiles idxs, starts, ends = maketiles(df.index.values, df.Start.values, sorted_nearest/src/tiles.pyx:24: in sorted_nearest.src.tiles.maketiles ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'long' but got 'long long' sorted_nearest/src/tiles.pyx:48: ValueError ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ________________________________ test_windows2 _________________________________ [gw2] linux -- Python 3.12.2 /usr/bin/python3.12 def test_windows2(): c = """Chromosome Start End Count 0 chr1 10200 10400 7 1 chr1 10400 10600 7 2 chr1 51400 51600 1 3 chr1 51600 51800 3 4 chr1 51800 52000 3""" df = pd.read_csv(StringIO(c), sep=r"\s+", nrows=5) # df.End -= 1 gr = pr.PyRanges(df) print(gr) > result = gr.tile(200) tests/windows/test_windows.py:48: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/pyranges.py:4649: in tile df = pyrange_apply_single(_tiles, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:40: in _tiles idxs, starts, ends = maketiles(df.index.values, df.Start.values, sorted_nearest/src/tiles.pyx:24: in sorted_nearest.src.tiles.maketiles ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'long' but got 'long long' sorted_nearest/src/tiles.pyx:48: ValueError ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+-----------+ | Chromosome | Start | End | Count | | (category) | (int32) | (int32) | (int64) | |--------------+-----------+-----------+-----------| | chr1 | 10200 | 10400 | 7 | | chr1 | 10400 | 10600 | 7 | | chr1 | 51400 | 51600 | 1 | | chr1 | 51600 | 51800 | 3 | | chr1 | 51800 | 52000 | 3 | +--------------+-----------+-----------+-----------+ Unstranded PyRanges object has 5 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome. =============================== warnings summary =============================== tests/conftest.py:83 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/conftest.py:83: SyntaxWarning: invalid escape sequence '\s' sep="\s+", pyranges/__init__.py:18 pyranges/__init__.py:18 pyranges/__init__.py:18 pyranges/__init__.py:18 pyranges/__init__.py:18 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/__init__.py:18: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources tests/test_binary.py:118 tests/test_binary.py:118 tests/test_binary.py:118 tests/test_binary.py:118 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:118: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:139 tests/test_binary.py:139 tests/test_binary.py:139 tests/test_binary.py:139 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:139: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:160 tests/test_binary.py:160 tests/test_binary.py:160 tests/test_binary.py:160 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:160: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:187 tests/test_binary.py:187 tests/test_binary.py:187 tests/test_binary.py:187 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:187: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:212 tests/test_binary.py:212 tests/test_binary.py:212 tests/test_binary.py:212 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:212: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:291 tests/test_binary.py:291 tests/test_binary.py:291 tests/test_binary.py:291 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:291: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:329 tests/test_binary.py:329 tests/test_binary.py:329 tests/test_binary.py:329 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:329: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:368 tests/test_binary.py:368 tests/test_binary.py:368 tests/test_binary.py:368 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:368: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:392 tests/test_binary.py:392 tests/test_binary.py:392 tests/test_binary.py:392 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:392: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:426 tests/test_binary.py:426 tests/test_binary.py:426 tests/test_binary.py:426 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:426: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:516 tests/test_binary.py:516 tests/test_binary.py:516 tests/test_binary.py:516 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:516: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:579 tests/test_binary.py:579 tests/test_binary.py:579 tests/test_binary.py:579 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:579: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) pyranges/methods/init.py:60: 20 warnings .pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py: 9 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 300874 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 47600 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 8 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_count_overlaps.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_getset_attr.py: 3 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_io.py: 4 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_pickle.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 6 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 4 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 24924 warnings .pybuild/cpython3_3.12_pyranges/build/tests/windows/test_windows.py: 2 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:60: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. return {k: v for k, v in df.groupby(grpby_key)} pyranges/methods/init.py:189: 16 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 2527 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 256 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 7 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 5724 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:189: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby("Chromosome") tests/test_do_not_error.py:46 tests/test_do_not_error.py:46 tests/test_do_not_error.py:46 tests/test_do_not_error.py:46 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py:46: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:35 tests/test_unary.py:35 tests/test_unary.py:35 tests/test_unary.py:35 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:35: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:100 tests/test_unary.py:100 tests/test_unary.py:100 tests/test_unary.py:100 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:100: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:163 tests/test_unary.py:163 tests/test_unary.py:163 tests/test_unary.py:163 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:163: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:205 tests/test_unary.py:205 tests/test_unary.py:205 tests/test_unary.py:205 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:205: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:234 tests/test_unary.py:234 tests/test_unary.py:234 tests/test_unary.py:234 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:234: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:272 tests/test_unary.py:272 tests/test_unary.py:272 tests/test_unary.py:272 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:272: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:287 tests/test_unary.py:287 tests/test_unary.py:287 tests/test_unary.py:287 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:287: HypothesisDeprecationWarning: The return_value health check is deprecated, because this is always an error. @settings( tests/test_unary.py:315 tests/test_unary.py:315 tests/test_unary.py:315 tests/test_unary.py:315 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:315: HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 47091 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 3877 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 6752 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/tostring2.py:31: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. df = pd.concat([plus, minus]) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 3238 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 5601 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:187: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby(["Chromosome", "Strand"]) .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for _, gdf in natsorted(df.groupby(groupby)): -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] FAILED tests/test_binary.py::test_set_intersect[False] - Exception: Starts/En... FAILED tests/test_binary.py::test_nearest[downstream-False-same] - ExceptionG... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] FAILED tests/test_binary.py::test_set_intersect[same] - Exception: Starts/End... FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] - Except... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] FAILED tests/test_binary.py::test_set_union[False] - Exception: Starts/Ends n... FAILED tests/test_binary.py::test_jaccard[False] - Exception: Starts/Ends not... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] FAILED tests/test_binary.py::test_set_union[same] - Exception: Starts/Ends no... FAILED tests/test_binary.py::test_jaccard[same] - Exception: Starts/Ends not ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] - Val... FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] - Va... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] - ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] - Valu... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] - Exc... FAILED tests/test_binary.py::test_coverage[False] - Exception: Starts/Ends no... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] - E... FAILED tests/test_binary.py::test_coverage[same] - Exception: Starts/Ends not... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] - Excep... FAILED tests/test_binary.py::test_coverage[opposite] - Exception: Starts/Ends... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] FAILED tests/test_binary.py::test_subtraction[same] - Exception: Starts/Ends ... FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] - Exce... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] FAILED tests/test_binary.py::test_subtraction[opposite] - Exception: Starts/E... FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] - Ex... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] FAILED tests/test_binary.py::test_subtraction[False] - Exception: Starts/Ends... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] - Except... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] - Value... FAILED tests/test_binary.py::test_nearest[None-True-False] - ExceptionGroup: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] - Value... FAILED tests/test_binary.py::test_nearest[None-True-same] - ExceptionGroup: H... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] - ValueErro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] - ValueErr... FAILED tests/test_binary.py::test_nearest[None-True-opposite] - ExceptionGrou... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] FAILED tests/test_binary.py::test_nearest[None-False-False] - ValueError: Buf... FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] - ValueE... FAILED tests/test_binary.py::test_nearest[None-False-same] - ValueError: Buff... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] - ValueError... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] - ValueErro... FAILED tests/test_binary.py::test_nearest[None-False-opposite] - ValueError: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest - ValueError: Buffer... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] FAILED tests/test_binary.py::test_nearest[upstream-True-False] - ExceptionGro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] FAILED tests/test_binary.py::test_nearest[upstream-True-same] - ExceptionGrou... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] - Exception... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] FAILED tests/test_binary.py::test_nearest[upstream-False-False] - ExceptionGr... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] FAILED tests/test_binary.py::test_nearest[upstream-False-same] - ExceptionGro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] - Exceptio... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] FAILED tests/test_binary.py::test_nearest[downstream-True-False] - ExceptionG... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] FAILED tests/test_binary.py::test_nearest[downstream-True-same] - ExceptionGr... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] - Excepti... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] FAILED tests/test_binary.py::test_nearest[downstream-False-False] - ValueErro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] FAILED tests/test_genomicfeatures.py::test_introns_single - ValueError: Buffe... FAILED tests/test_unary.py::test_merge[True] - Exception: Starts/Ends not int... FAILED tests/test_unary.py::test_cluster[True] - Exception: Starts/Ends not i... FAILED tests/test_unary.py::test_merge[False] - Exception: Starts/Ends not in... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] FAILED tests/test_unary.py::test_cluster[False] - Exception: Starts/Ends not ... FAILED tests/test_unary.py::test_windows - Exception: Starts/Ends not int64 o... FAILED tests/test_unary.py::test_summary - Exception: Starts/Ends not int64 o... FAILED tests/windows/test_windows.py::test_windows - ValueError: Buffer dtype... FAILED tests/windows/test_windows.py::test_windows2 - ValueError: Buffer dtyp... ======== 410 failed, 121 passed, 450644 warnings in 35822.27s (9:57:02) ======== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 4 I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/*.bed /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/test_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges '/build/reproducible-path/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/chip_10.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/gencode.gff3' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/test_sorted.bam' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/exons.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/bw.bw' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/cpg.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/lamina.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chipseq.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/aorta.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/aorta2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/control.bam' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/control.bam.bai' I: pybuild base:305: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build; python3.11 -m pytest -v -n 4 ============================= test session starts ============================== platform linux -- Python 3.11.8, pytest-8.1.1, pluggy-1.4.0 -- /usr/bin/python3.11 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/.hypothesis/examples')) rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: hypothesis-6.99.9, xdist-3.5.0 created: 4/4 workers 4 workers [531 items] scheduling tests via LoadScheduling tests/test_binary.py::test_nearest[downstream-False-same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/data/test_data.py::test_all_data [gw0] [ 0%] PASSED tests/data/test_data.py::test_all_data tests/test_binary.py::test_set_intersect[False] [gw3] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] [gw2] [ 0%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] [gw3] [ 0%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] [gw0] [ 0%] FAILED tests/test_binary.py::test_set_intersect[False] tests/test_binary.py::test_set_intersect[same] [gw1] [ 1%] FAILED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_nearest[downstream-False-opposite] [gw2] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] [gw3] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] [gw1] [ 1%] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_binary.py::test_jaccard[False] [gw0] [ 1%] FAILED tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_set_union[False] [gw2] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] [gw3] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] [gw1] [ 2%] FAILED tests/test_binary.py::test_jaccard[False] tests/test_binary.py::test_jaccard[same] [gw0] [ 2%] FAILED tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_set_union[same] [gw2] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] [gw3] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] [gw1] [ 3%] FAILED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw0] [ 3%] FAILED tests/test_binary.py::test_set_union[same] tests/test_binary.py::test_overlap[False] [gw2] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] [gw3] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] [gw1] [ 3%] PASSED tests/test_binary.py::test_join[False] tests/test_binary.py::test_join[same] [gw0] [ 4%] PASSED tests/test_binary.py::test_overlap[False] tests/test_binary.py::test_overlap[same] [gw2] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] [gw1] [ 4%] PASSED tests/test_binary.py::test_join[same] tests/test_binary.py::test_join[opposite] [gw0] [ 4%] PASSED tests/test_binary.py::test_overlap[same] tests/test_binary.py::test_overlap[opposite] [gw3] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] [gw2] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] [gw0] [ 5%] PASSED tests/test_binary.py::test_overlap[opposite] tests/test_binary.py::test_intersect[False] [gw1] [ 5%] PASSED tests/test_binary.py::test_join[opposite] tests/test_binary.py::test_reldist [gw2] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] [gw1] [ 5%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw3] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw0] [ 6%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_intersect[same] [gw2] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] [gw0] [ 6%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw1] [ 6%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw3] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] [gw2] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] [gw0] [ 7%] PASSED tests/test_binary.py::test_intersect[opposite] tests/test_binary.py::test_coverage[False] [gw1] [ 7%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw3] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] [gw3] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] [gw2] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] [gw0] [ 8%] FAILED tests/test_binary.py::test_coverage[False] tests/test_binary.py::test_coverage[same] [gw1] [ 8%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] [gw2] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] [gw3] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] [gw3] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] [gw0] [ 9%] FAILED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_coverage[opposite] [gw1] [ 9%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw2] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] [gw3] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] [gw3] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] [gw0] [ 10%] FAILED tests/test_binary.py::test_coverage[opposite] tests/test_binary.py::test_subtraction[same] [gw1] [ 10%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw2] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] [gw3] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] [gw0] [ 10%] FAILED tests/test_binary.py::test_subtraction[same] tests/test_binary.py::test_subtraction[opposite] [gw1] [ 11%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw2] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] [gw3] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] [gw2] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] [gw0] [ 11%] FAILED tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_subtraction[False] [gw1] [ 12%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] tests/test_binary.py::test_k_nearest[upstream-False-same-last] [gw3] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] [gw2] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] [gw0] [ 12%] FAILED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw2] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] [gw1] [ 12%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw3] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] [gw0] [ 13%] FAILED tests/test_binary.py::test_nearest[None-True-False] tests/test_binary.py::test_nearest[None-True-same] [gw2] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] [gw2] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] [gw1] [ 13%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw3] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] [gw0] [ 14%] FAILED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw2] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] [gw1] [ 14%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_binary.py::test_k_nearest[upstream-True-same-last] [gw3] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] [gw0] [ 15%] FAILED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw2] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] [gw1] [ 15%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw3] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] [gw0] [ 15%] FAILED tests/test_binary.py::test_nearest[None-False-False] tests/test_binary.py::test_nearest[None-False-same] [gw1] [ 16%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw2] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] [gw3] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] [gw0] [ 16%] FAILED tests/test_binary.py::test_nearest[None-False-same] tests/test_binary.py::test_nearest[None-False-opposite] [gw1] [ 16%] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] tests/test_binary.py::test_k_nearest[None-False-same-last] [gw2] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] [gw3] [ 17%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] [gw0] [ 17%] FAILED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_nearest[upstream-True-False] [gw1] [ 17%] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] tests/test_binary.py::test_k_nearest[None-False-False-last] [gw2] [ 17%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] [gw3] [ 17%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] [gw0] [ 18%] FAILED tests/test_binary.py::test_nearest[upstream-True-False] tests/test_binary.py::test_nearest[upstream-True-same] [gw1] [ 18%] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw3] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] [gw2] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] [gw1] [ 18%] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] tests/test_binary.py::test_k_nearest[None-True-same-last] [gw0] [ 19%] FAILED tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw3] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] [gw1] [ 19%] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] tests/test_binary.py::test_k_nearest[None-True-False-last] [gw2] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] [gw0] [ 19%] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw3] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] [gw1] [ 20%] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw2] [ 20%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw0] [ 20%] FAILED tests/test_binary.py::test_nearest[upstream-False-False] tests/test_binary.py::test_nearest[upstream-False-same] [gw1] [ 20%] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest tests/test_change_chromosome_custom.py::test_change_chromosomes [gw1] [ 20%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw1] [ 21%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw1] [ 21%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_concat.py::test_concat_unstranded_stranded [gw1] [ 21%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw1] [ 21%] PASSED tests/test_count_overlaps.py::test_strand_vs_strand_same tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw3] [ 21%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] [gw2] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] [gw2] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] [gw0] [ 22%] FAILED tests/test_binary.py::test_nearest[upstream-False-same] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw1] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] [gw1] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] [gw3] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] [gw2] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] [gw0] [ 23%] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] tests/test_binary.py::test_nearest[downstream-True-False] [gw2] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] [gw1] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] [gw3] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] [gw1] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] [gw3] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] [gw3] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] [gw0] [ 24%] FAILED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_binary.py::test_nearest[downstream-True-same] [gw2] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] [gw1] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] [gw3] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] [gw0] [ 25%] FAILED tests/test_binary.py::test_nearest[downstream-True-same] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw2] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] [gw3] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] [gw1] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] [gw0] [ 26%] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw2] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] [gw3] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] [gw0] [ 26%] FAILED tests/test_binary.py::test_nearest[downstream-False-False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] [gw1] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] [gw2] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] [gw2] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] [gw3] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] [gw0] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] [gw1] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] [gw0] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] [gw3] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] [gw2] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] [gw2] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] [gw0] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw1] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] [gw0] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] [gw3] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] [gw2] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] [gw2] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] [gw0] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] [gw1] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] [gw3] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] [gw2] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] [gw0] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] [gw3] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] [gw1] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] [gw0] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] [gw2] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] [gw1] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] [gw3] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] [gw3] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] [gw3] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] [gw3] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] [gw0] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] [gw1] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] [gw1] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] [gw2] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] [gw0] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] [gw3] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw3] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] [gw0] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] [gw2] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] [gw1] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] [gw1] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] [gw3] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] [gw0] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] [gw2] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] [gw1] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] [gw1] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] [gw3] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] [gw0] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] [gw1] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] [gw2] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] [gw0] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] [gw3] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] [gw1] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] [gw2] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] [gw0] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] [gw1] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] [gw3] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] [gw2] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] [gw0] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] [gw1] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] [gw3] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] [gw0] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] [gw2] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] [gw2] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] [gw1] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] [gw3] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] [gw0] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] [gw2] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] [gw2] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] [gw3] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw0] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] [gw1] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] [gw2] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw2] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] [gw3] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] [gw0] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] [gw1] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] [gw2] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] [gw0] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] [gw1] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] [gw3] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] [gw0] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] [gw3] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] [gw0] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] [gw3] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] [gw0] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] [gw3] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] [gw2] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] [gw1] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] [gw1] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] [gw0] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] [gw1] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] [gw0] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] [gw3] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] [gw1] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] [gw2] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw3] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] [gw2] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] [gw1] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] [gw3] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] [gw0] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] [gw1] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] [gw2] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] [gw3] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] [gw1] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw0] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] [gw2] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] [gw3] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] [gw1] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] [gw0] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] [gw2] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] [gw1] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] [gw0] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] [gw3] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] [gw2] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] [gw1] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] [gw3] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] [gw0] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] [gw2] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] [gw1] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] [gw2] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] [gw3] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] [gw0] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] [gw1] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] [gw0] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] [gw3] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] [gw2] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] [gw2] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] [gw1] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw0] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] [gw3] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] [gw1] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] [gw2] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] [gw2] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] [gw3] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] [gw0] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] [gw3] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] [gw1] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] [gw0] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] [gw0] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] [gw2] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] [gw0] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] [gw3] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] [gw1] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] [gw2] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] [gw0] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw0] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] [gw3] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] [gw1] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] [gw2] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] [gw0] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] [gw3] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] [gw1] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] [gw2] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] [gw0] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] [gw3] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] [gw1] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] [gw1] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] [gw2] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] [gw0] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] [gw3] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] [gw1] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] [gw2] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw3] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] [gw0] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] [gw1] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] [gw2] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] [gw3] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] [gw3] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] [gw0] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] [gw1] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] [gw2] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] [gw3] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] [gw0] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] [gw3] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] [gw1] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] [gw2] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] [gw3] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] [gw0] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] [gw2] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] [gw3] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] [gw1] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] [gw2] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] [gw0] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] [gw1] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] [gw3] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] [gw2] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw0] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] [gw0] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] [gw1] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] [gw3] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] [gw2] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] [gw1] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] [gw0] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] [gw3] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] [gw0] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] [gw2] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] [gw3] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw1] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] [gw1] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] [gw0] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] [gw2] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] [gw0] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] [gw3] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] [gw0] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] [gw2] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] [gw1] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] [gw2] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] [gw1] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw3] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw0] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] [gw1] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] [gw1] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] [gw2] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] [gw2] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] [gw3] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] [gw0] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] [gw1] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] [gw2] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] [gw2] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] [gw3] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] [gw0] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] [gw1] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] [gw2] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] [gw3] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] [gw0] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] [gw3] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] [gw3] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] [gw3] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] [gw1] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] [gw2] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] [gw0] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] [gw3] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] [gw1] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] [gw2] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] [gw0] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] [gw3] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] [gw1] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] [gw2] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] [gw0] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] [gw3] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] [gw1] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] [gw0] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] [gw2] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw3] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] [gw1] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] [gw0] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] [gw2] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] [gw3] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] [gw2] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] [gw1] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] [gw3] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] [gw0] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] [gw1] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] [gw2] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] [gw3] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] [gw2] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] [gw3] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] [gw0] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] [gw1] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw0] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] [gw2] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] [gw3] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] [gw3] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] [gw2] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] Sat Mar 30 14:18:19 UTC 2024 - pbuilder was killed by timeout after 18h.